Transcription activation complex and utilization thereof

ABSTRACT

The present invention provides a complex of the transcription coupling factor of any of ARNT 1 to 3 and the transcription regulatory factor comprising any of the amino acid sequence from the amino acid sequence group comprising for example the amino acid sequences represented by SEQ ID Nos.1 to 3, which is a transcription activating complex having an ability of binding to a DNA region (5′-ACGTG-3′, SEQ ID No.16) to which a transcription inhibiting complex of the transcription coupling factor and a Sim2 as a transcription regulatory factor can be bound and having an ability of promoting the transcription of a gene located downstream of the DNA region.

TECHNICAL FIELD

The present invention relates to a transcription activation complex and utilization thereof.

BACKGROUND ART

Down's syndrome is one of the most frequent diseases relating to autosomal aberrations. A Down's syndrome patients has the chromosome No.21 in a somatic cell which is not a normal duplicate chromosome but is a trisomy (triplicate), which leads to a mental retardation, abnormal development, heart disease, leukemia, early Alzheimer's disease.

The results of many investigations made so far on the isolation, identification and functional analysis of the causative genes of this disease indicated that (1) the gene of Single-minded 2 (hereinafter designated as Sim2) known as a transcription regulatory factor playing an important role in the development and differentiation of a central nervous system cell is present in a critical region (q22.2) for the Down's syndrome on the human chromosome No.21, that (2) an increased Sim2 gene expression product in a cell is suggested to be a pathogenic component of the Down's syndrome since the Down's syndrome becomes symptomatic even when only this narrow critical region becomes trisomy, and that (3) a transcription inhibiting complex formed as a result of the binding between a transcription coupling factor classified into an ARNT family such as ARNT1 or ARNT2 (hereinafter sometimes referred to as an ARNT family transcription coupling factor) and a Sim2 exhibits an inhibitory action on a CME sequence (5′-ACGTG-3′: a core sequence of an element required for the transcription in the midline in the central nervous system, which is the nucleotide sequence of a DNA to which the protein complex of this transcription coupling factor with the Sim2 can be bound), and more typically, an investigation of the Sim2 function for the activity on the transcription of a reporter gene comprising a CME sequence-carrying promoter bound functionally thereto revealed that the Sim2 has a potent inhibitory effect even on the transcription activity of an ARNT family coupling factor which is an auxiliary factor as its binding partner (i.e., transcription coupling factor) and a Sim2/ARNT family transcription coupling factor heterodimer complex (i.e., a transcription inhibiting complex formed as a result of the binding between the ARNT family transcription coupling factor and the Sim2) was revealed to have an inhibitory effect on the CME sequence, and the promotion of the transcription inhibition by this transcription inhibiting complex is now considered to be one of the causes of the Down's syndrome.

Based on the findings discussed above, a transcription activating complex allowing a transcription regulatory factor/ARNT family transcription coupling factor heterodimer complex to exhibit a promotive activity on the CME sequence has been desired to be found and forced to act competitively against the Sim2/ARNT family transcription coupling factor heterodimer complex, whereby achieving an application to the treatment of the Down's syndrome.

DISCLOSURE OF THE INVENTION

We made effort under such a circumstance and finally discovered that the complex of a certain ARNT family transcription coupling factor and a certain transcription regulatory factor has an ability of exerting a promotive activity on the CME sequence, whereby establishing the present invention.

Thus, the invention provides:

1. a complex of the transcription coupling factor of any of ARNT 1 to 3 and the transcription regulatory factor comprising any of the amino acid sequences shown below (hereinafter sometimes referred to as a present amino acid sequences), which is a transcription activating complex (hereinafter sometimes referred to as an inventive transcription activating complex) having an ability of binding to a DNA region (5′-ACGTG-3′, SEQ ID No.16) to which a transcription inhibiting complex of a Sim2 as a transcription regulatory factor and the transcription coupling factor can be bound and having an ability of promoting the transcription of a gene located downstream of the DNA region, wherein the amino acid sequences are;

<<Amino Acid Sequence Group>>

(a) the amino acid sequence represented by any of SEQ ID Nos.1 to 3,

(b) the amino acid sequence of a protein comprising an amino acid sequence exhibiting an amino acid identity of 90% or more to the amino acid sequence represented by any of SEQ ID Nos.1 to 3 and also having a transcription regulation ability,

(c) the amino acid sequence of a protein comprising an amino acid sequence encoded by a DNA which hybridizes under a stringent condition with a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 102 to 2507 in the nucleotide sequence represented by SEQ ID No.4 and also having a transcription regulation ability,

(d) the amino acid sequence of a protein comprising an amino acid sequence encoded by a DNA which hybridizes under a stringent condition with a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 51 to 2456 in the nucleotide sequence represented by SEQ ID No.5 and also having a transcription regulation ability,

(e) the amino acid sequence a protein comprising an amino acid sequence encoded by a DNA which hybridizes under a stringent condition with a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 35 to 2440 in the nucleotide sequence represented by SEQ ID No.6 and also having a transcription regulation ability;

2. a transformant (hereinafter sometimes referred to as an inventive transformant) obtainable by introducing one or more vectors (hereinafter sometimes generally referred to as present vector) having an ability of producing a transcription activating complex according to above-mentioned 1 into a host cell;

3. a transformant obtainable by introducing a single vector comprising the both of the DNAs shown below or several vectors comprising such DNAs independently into a host cell, wherein the DNAs are:

<<DNAs >>

(1) the DNA comprising a nucleotide sequence encoding the amino acid sequence of the transcription coupling factor of any of ARNT 1 to 3;

(2) the DNA comprising a nucleotide sequence encoding a present amino acid sequence;

4. A transformant according to the above-mentioned 2 or 3 further containing the DNA of a reporter gene comprising a promoter, as being operably connected thereto, said promoter contains DNA region (5′-ACGTG-3′, SEQ ID No.16) to which the transcription inhibiting complex of the Sim2 as a transcription regulatory factor and the transcription coupling factor of any of ARNT 1 to 3 can be bound;

5. a method (hereinafter sometimes referred to as an inventive evaluation method) for evaluating an ability of regulating a transcription promoting ability (hereinafter sometimes referred to as a present regulating ability) possessed by a transcription activating complex according to the above-mentioned 1, which comprises:

(1) a first step for bringing a test substance into contact with a transformant according to the above-mentioned 4;

(2) a second step, after the first step, for measuring the expression level of the reporter gene possessed by the transformant or an index value correlating with the level; and,

(3) a third step for evaluating the substance for its ability of regulating the transcription promoting ability possessed by the transcription activating complex based on the expression level or the index value correlating with the level measured in the second step;

6. a searching method (hereinafter sometimes referred to as an inventive searching method) comprising a step for selecting a substance having an ability of regulating the transcription promoting ability possessed by the transcription activating complex based on a regulating ability evaluated by the method according to the above-mentioned 5;

7. a therapeutic agent (hereinafter sometimes referred to as an inventive therapeutic agent) containing as an active ingredient a substance searched for by a method according to the above-mentioned 6 or a pharmaceutically acceptable salt thereof;

8. a therapeutic agent according to the above-mentioned 7 which is a Down's syndrome improving agent;

9. a use as a Down's syndrome improving agent a single vector comprising the both of the DNAs shown below or several vectors comprising said DNAs independently, wherein the DNAs are:

<<DNAs >>

(1) the DNA comprising a nucleotide sequence encoding the amino acid sequence of the transcription coupling factor of any of ARNT 1 to 3;

(2) the DNA comprising a nucleotide sequence encoding a present amino acid sequence;

10. a transcription activating complex (hereinafter sometimes referred to as an inventive transcription activating complex 2) containing a protein comprising one member (A or B) among the member I shown below and one member (X or Y) among the member II shown below and a protein comprising the other member (B or A) among the member I shown below and the other member (Y or X) among the member II shown below, the formation of the complex with the both protein being under the control by the ligand, the member I being:

<<Member I>>

(A) a region to which a transcription regulatory factor comprising any of the following amino acid sequences is bound in the transcription coupling factor of any of ARNT 1 to 3; or,

(B) a region to which the transcription coupling factor of any of ARNT 1 to 3 is bound in a transcription regulatory factor comprising a present amino acid sequence; the member II being:

<<Member II>>

(X) a DNA binding region of a transcription regulatory factor which is functional in a host cell; or,

(Y) a transcription activating region of a transcription regulatory factor which is functional in a host cell;

11. a transcription activating complex according to the above-mentioned 10 wherein the (X) among the member II is bound to a DNA consisting of any of the nucleotide sequences shown below, the DNA sequence group being:

<<DNA Sequence Group>>

(1) the nucleotide sequence of the DNA to which a Gal4 protein is bound (5′-CGGAGGACTGTCCTCCG-3′, SEQ ID No.11);

(2) the nucleotide sequence of the DNA to which a Lex protein is bound (5′-TACTGTATGTACATACAGTA-3′, SEQ ID No.12);

(3) the nucleotide sequence of the DNA to which a Lac I receptor protein is bound (5′-GAATTGTGAGCGCGCACAATTC-3′, SEQ ID No.13);

(4) the nucleotide sequence of the DNA to which a tetracyclin receptor protein is bound (5′-TCGAGTTTACCACTCCCTATCAGTGATAGAGAAAAGTGAAAG-3′, SEQ ID No.14); or,

(5) the nucleotide sequence of the DNA to which a ZFHD-1 protein is bound (5′-TAATGATGGGCG-3′, SEQ ID No.15);

(6) the nucleotide sequence of the DNA to which a transcription inhibiting complex of the transcription coupling factor of any of ARNT 1 to 3 with the Sim2 as a transcription regulatory factor can be bound (5′-ACGTG-3′, SEQ ID No.16);

12. a transcription activating complex according to the above-mentioned 10 wherein the (Y) among the member II is derived from any of the following proteins, the proteins being:

<<Proteins>>

(1) a Gal4 protein;

(2) a Lex protein;

(3) a Lac I receptor protein;

(4) a tetracyclin receptor protein;

(5) a ZFHD-1 protein;

(6) a B42 protein;

(7) a protein as a transcription coupling factor of any of ARNT 1 to 3;

(8) a VP16 protein;

13. a transcription activating complex according to the above-mentioned 10 wherein the both proteins formed said complex under the control of a ligand;

14. a transcription activating complex according to the above-mentioned 13 wherein the (B) among the member I has a region to which the ligand is bound;

15. a transformant (hereinafter sometimes referred to as an inventive transformant 2) obtainable by introducing;

(1) one member (a or b) among the member i shown below and one member (x or y) among the member ii shown below;

(2) the other member (b or a) among the member i shown below and the other member (y or x) among the member ii shown below; and;

(3) the member iii shown below,

the member i being:

<<Member i>>

(a) the DNA comprising a nucleotide sequence encoding the amino acid sequence of the region to which a transcription regulatory factor comprising a present amino acid sequence is bound in the transcription coupling factor of any of ARNT 1 to 3;

(b) the DNA comprising a nucleotide sequence encoding the amino acid sequence of the region to which the transcription coupling factor of any of ARNT 1 to 3 is bound in the transcription regulatory factor comprising any of the amino acid sequences shown below; the member ii being:

<<Member ii>>

(X) a DNA comprising a nucleotide sequence encoding the amino acid sequence of a DNA binding region of a transcription regulatory factor which is functional in a host cell; or,

(Y) a DNA comprising a nucleotide sequence encoding the amino acid sequence of a transcription activating region of a transcription regulatory factor which is functional in a host cell;

the member iii being:

<<Member iii>>

a DNA comprising a reporter gene connected to the downstream of the promoter, said promoter contains a DNA to which a DNA binding region comprising the amino acid sequence encoded by the nucleotide sequence of (x) among the member ii can be bound;

16. a transformant according to the above-mentioned 15 wherein the (x) among the member ii is a DNA comprising the nucleotide sequence encoding the amino acid sequence of a protein which binds to the DNA consisting of any of the nucleotide sequences shown below, the nucleotide sequences being:

<<Nucleotide Sequence Group>>

(1) the nucleotide sequence of the DNA to which a Gal4 protein is bound (5′-CGGAGGACTGTCCTCCG-3′, SEQ ID No.11);

(2) the nucleotide sequence of the DNA to which a Lex protein is bound (5′-TACTGTATGTACATACAGTA-3′, SEQ ID No.12);

(3) the nucleotide sequence of the DNA to which a Lac I receptor protein is bound (5′-GAATTGTGAGCGCGCACAATTC-3′, SEQ ID No.13);

(4) the nucleotide sequence of the DNA to which a tetracyclin receptor protein is bound (5′-TCGAGTTTACCACTCCCTATCAGTGATAGAGAAAAGTGAAAG-3′, SEQ ID No.14); or,

(5) the nucleotide sequence of the DNA to which a ZFHD-1 protein is bound (5′-TAATGATGGGCG-3′, SEQ ID No.15);

(6) the nucleotide sequence of the DNA to which a transcription inhibiting complex of the transcription coupling factor of any of ARNT 1 to 3 with the Sim2 as a transcription regulatory factor can be bound (5′-ACGTG-3′, SEQ ID No.16);

17. a transformant according to the above-mentioned 15 wherein the (y) among the member ii is derived from a DNA comprising the nucleotide sequence encoding the amino acid sequence of any of the proteins shown below, the proteins being:

<<Proteins>>

(1) a Gal4 protein;

(2) a Lex protein;

(3) a Lac I receptor protein;

(4) a tetracyclin receptor protein;

(5) a ZFHD-1 protein;

(6) a B42 protein;

(7) a protein as a transcription coupling factor of any of ARNT 1 to 3;

(8) a VP16 protein;

18. a use of a transcription activating complex according to the above-mentioned 1 or 10 for a two-hybrid assay;

19. a use of a transformant according to the above-mentioned 3 or 15 for a two-hybrid assay;

20. a receptor binding assay (hereinafter sometimes referred to as an inventive binding assay) comprising the steps:

(1) a step for bringing a transcription activating complex according to the above-mentioned 10 to which a labeled ligand is bound into contact with a test substance; and,

(2) a step for an indirect verification of the state of the binding between the transcription activating complex and the test substance by means of monitoring the level of a ligand in a free form or a ligand in a binding form generated as a result of the competition between the labeled ligand and the test substance or an index value correlating with the level; and the like.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the results of a two-hybrid assay (system employing Gal4-NXF+VP16-X) for verifying the formation of the complex of a present ARNT family transcription coupling factor and a present transcription regulatory factor. The abscissa represents a transcription coupling factor and the like employed in each test system. Those up to the third from the left end are of the present ARNT family transcription coupling factor. Those from the fourth to the sixth from the left end are of the non-present ARNT family transcription coupling factor, which correspond to the test system for comparison. The second from the right end is of a present transcription regulatory factor (NXF) which corresponds to the test system for investigating whether a homodimer is formed or not. The right end is of a CP, which corresponds to the test system for a negative control. The ordinate represents a luciferase activity level, which is an index value representing an activity on the transcription of a reporter gene.

FIG. 2 shows the results of a two-hybrid assay (system employing Gal4-Arnt1+VP16-X) for verifying the formation of the complex of an ARNT 1 as a present ARNT family transcription coupling factor and a present transcription regulatory factor. The abscissa represents a transcription regulatory factor employed in each test system. The left end is of a Sim2, which corresponds to the test system for a positive control. The second from the left end was of a Clock, which corresponds to the test system for a comparison. The second from the right end is of a present transcription regulatory factor (NXF). The right end is of a CP, which corresponds to the test system for a negative control. The ordinate represents a luciferase activity level, which is an index value representing an activity on the transcription of a reporter gene.

FIG. 3 shows the results of a two-hybrid assay (system employing Gal4-Arnt2+VP16-X) for verifying the formation of the complex of an ARNT 2 as a present ARNT family transcription coupling factor and a present transcription regulatory factor. The abscissa represents a transcription regulatory factor employed in each test system. The left end is of a present transcription regulatory factor (NXF). The right end is of a CP, which corresponds to the test system for a negative control. The ordinate represents a luciferase activity level, which is an index value representing an activity on the transcription of a reporter gene.

FIG. 4 shows the results of a two-hybrid assay (system employing Gal4-Arnt3+VP16-X) for verifying the formation of the complex of an ARNT 3 as a present ARNT family transcription coupling factor and a present transcription regulatory factor. The abscissa represents a transcription regulatory factor employed in each test system. The left end is of a present transcription regulatory factor (NXF). The right end is of a CP, which corresponds to the test system for a negative control. The ordinate represents a luciferase activity level, which is an index value representing an activity on the transcription of a reporter gene.

FIG. 5 shows the results of a two-hybrid assay (system employing Gal4-Bmal2+VP16-X) for verifying the formation of the complex of a Bmal2 as a non-present ARNT family transcription coupling factor and a present transcription regulatory factor. The abscissa represents a transcription regulatory factor employed in each test system. The left end is of a Clock, which corresponds to the test system for a positive control. The midst is of a present transcription regulatory factor (NXF). The right end is of a CP, which corresponds to the test system for a negative control. The ordinate represents a luciferase activity level, which is an index value representing an activity on the transcription of a reporter gene.

FIG. 6 shows the results of a gel sift assay for verifying the DNA binding ability possessed by an inventive transcription activating complex. Lane 1 employs only a probe as a sample, Lane 2 employs as a sample a total cell extract prepared from a cell infected with a wild Baculovirus (non-recombinant virus), Lane 3 employs as a sample a total cell extract containing an Arnt2 which is a present ARNT family transcription coupling factor, Lane 4 employs as a sample a total cell extract containing a present transcription regulatory factor (NXF), Lane 5 employs as a sample a total cell extract containing an Arnt2 which is a present ARNT family transcription coupling factor together with a present transcription regulatory factor (NXF) (i.e., corresponding to an inventive transcription activating complex), Lane 6 employs as a sample a total cell extract containing an inventive transcription activating complex (i.e., Arnt2 and NXF) when allowing a large excess of a non-radiolabeled CME double-stranded oligonucleotide as a Cold probe DNA to coexist in the binding reaction system and Lane 7 employs as a sample a total cell extract containing an inventive transcription activating complex (i.e., Arnt2 and NXF) when allowing a large excess of a non-radiolabeled E-box double-stranded oligonucleotide as a Cold probe DNA to coexist in the binding reaction system. Each of Lanes 5 and 7 exhibits a band indicating a specific binding (a band indicating the binding with a hot probe DNA).

FIG. 7 shows the results of a reporter assay for verifying the transcription promoting ability of an inventive transcription activating complex. The abscissa represents a combination of an responsive sequence with a transcription regulatory factor and/or a transcription coupling factor plus transcription regulatory factor employed in each test system. Those up to the fourth from the left end are of the system employing an E-box sequences which is a Clock responsive sequence, which corresponds to the test system for comparison. On the other hand, those starting from the fifth from the left end are of the system employing a CME sequence, which corresponds to the test system according to the invention. The ordinate represents a luciferase activity level, which is an index value representing an activity on the transcription of the reporter gene. The right end indicates a potent transcription promoting ability of an inventive transcription activating complex (i.e., a coexpression of an Arnt2 which is a present ARNT family transcription coupling factor together with a present transcription regulatory factor (NXF)) on the reporter gene under the control of the CME sequence.

FIG. 8 shows the results of a reporter assay (in a system employing a reporter gene bound to a CME sequence-carrying promoter in a functional manner) for verifying the transcription promoting ability of an inventive transcription activating complex. The abscissa represents a combination of an Arnt2 which is a present ARNT family transcription coupling factor with any of various transcription regulatory factors (Clock, NXF or Sim2). Those up to the fourth (A, B, C, D) from the left end correspond to the test system for the dose dependency of the present transcription regulatory factor (NXF)-induced reporter gene transcription activity in the presence of the Arnt2 which is a present ARNT family transcription coupling factor. Those from the fifth to the eighth (E, F, G, H) from the left end correspond to the test system for the Sim2 influence on the present transcription regulatory factor (NXF)-induced reporter gene transcription activity in the presence of the Arnt2 which is a present ARNT family transcription coupling factor. Those from the ninth to the twelfth (I, J, K, L) from the left end correspond to the test system for the Clock influence on the present transcription regulatory factor (NXF)-induced reporter gene transcription activity in the presence of the Arnt2 which is a present ARNT family transcription coupling factor.

FIG. 9 shows the results of a reporter assay (in a system employing a reporter gene bound to a CME sequence-carrying promoter in a functional manner) for verifying the transcription promoting ability of an inventive transcription activating complex. The abscissa represents a combination of an Arnt2 which is a present ARNT family transcription coupling factor with any of various transcription regulatory factors (NXF and/or Sim2). Those starting from the second (b, c, d, e) from the left end correspond to the test system for the influence of a present transcription regulatory factor (NXF) on the present transcription regulatory factor (NXF)-induced reporter gene transcription activity in the presence of a Sim2 when an Arnt2 which is a present ARNT family transcription coupling factor is coexisting. The left end (a) is of the test system relating to the present transcription regulatory factor (NXF)-induced reporter gene transcription activity in the absence of a transcription regulating factor Sim2 when an Arnt2 which is a present ARNT family transcription coupling factor is coexisting, which corresponds to a control.

BEST MODE FOR CARRYING OUT THE INVENTION

The present invention is further detailed below.

An inventive transcription activating complex is a complex of the transcription coupling factor of any of ARNT 1 to 3 (hereinafter sometimes referred to as a present ARNT family transcription coupling factor) and the transcription regulatory factor (hereinafter sometimes referred to as a present transcription regulatory factor) comprising any of the amino acid sequences shown below (i.e., present amino acid sequences), which is a transcription activating complex having an ability of binding to a DNA region (5′-ACGTG-3′, SEQ ID No.16) to which a transcription inhibiting complex of a Sim2 as a transcription regulatory factor and the transcription coupling factor can be bound and having an ability of promoting the transcription of a gene located downstream of the DNA region.

<<Amino Acid Sequence Group>>

(a) the amino acid sequence represented by any of SEQ ID Nos.1 to 3 (the transcription regulatory factor comprising the amino acid sequence represented by SEQ ID No.1 is a present transcription regulatory factor derived from a human and sometimes designated as an hNXF; the transcription regulatory factor comprising the amino acid sequence represented by SEQ ID No.2 is a present transcription regulatory factor derived from a mouse and sometimes designated as an mNXF; and the transcription regulatory factor comprising the amino acid sequence represented by SEQ ID No.3 is a present transcription regulatory factor derived from a rat and sometimes designated as an rNXF);

(b) the amino acid sequence of a protein comprising an amino acid sequence exhibiting an amino acid identity of 90% or more to the amino acid sequence represented by any of SEQ ID Nos.1 to 3 and also having a transcription regulation ability,

(c) the amino acid sequence of a protein comprising an amino acid sequence encoded by a DNA which hybridizes under a stringent condition with a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 102 to 2507 in the nucleotide sequence represented by SEQ ID No.4 and also having a transcription regulation ability,

(d) the amino acid sequence of a protein comprising an amino acid sequence encoded by a DNA which hybridizes upper a stringent condition with a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 51 to 2456 in the nucleotide sequence represented by SEQ ID No.5 and also having a transcription regulation ability,

(e) the amino acid sequence a protein comprising an amino acid sequence encoded by a DNA which hybridizes under a stringent condition with a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 35 to 2440 in the nucleotide sequence represented by SEQ ID No.6 and also having a transcription regulation ability.

A protein forming an inventive transcription activating complex, i.e., a transcription coupling factor of any of ARNT1 to 3 is any ARNT family transcription coupling factor such as an ARNT1, ARNT2 and ARNT3 (identical to BMAL 1). Such a transcription coupling factor is a transcription coupling factor having a high sequence identity when compared with each other. Such a transcription coupling factor forms a transcription inhibiting complex together with a transcription regulatory factor Sim2, whereby possessing an ability of binding the DNA region represented by SEQ ID No.16 (5′-ACGTG-3′) and possessing an ability of inhibiting the transcription of a gene located downstream of the DNA region. Among such transcription coupling factors, those exemplified preferably are ARNT1 and ARNT2.

With regard to the other protein which forms an inventive transcription activating complex, the difference from the amino acid sequence represented by SEQ ID No. 1 to 3 observed in the amino acid sequence (i.e., present amino acid sequence) of the “transcription regulatory factor comprising any of the amino acid sequences shown below” may for example be the amino acid deletion, substitution, modification and addition. Any of such difference may be a variation introduced artificially by means of a site-directed mutagenesis and a mutagenic treatment, as well as a naturally occurring polymorphic variation such as a difference in the amino acid sequence due to the difference between the animal species, individuals, organs and tissues.

In the invention, the “amino acid identity” means an identity and a homology in the amino acid sequence between two proteins. The “amino acid identity” described above can be determined by comparing two amino acid sequence which are aligned optimally over the entire range of a reference amino acid. A reference protein here may have an addition or deletion (for example, a gap) in the optimal alignment of the two amino acid sequences. Such an amino acid identity can be calculated for example by producing an alignment utilizing a Clustal W algorism [Nucleic Acid Res., 22 (22): 4673-4680 (1994)] using a Vector NTI. The amino acid identity can be investigated also by using a sequence analysis software, typically Vector NTI, GENETYX-MAC or any other analytical tools provide DNA public database.

A preferred amino acid identity in the invention may for example be 90% or higher.

A “DNA which hybridizes under a stringent condition” described above may for example be a DNA capable of maintaining a hybrid, which was formed previously as a DNA-DNA hybrid by a hybridization at 65° C. at a high ion concentration [for example using 6×SSC (900 mM sodium chloride, 90 mM sodium citrate)], even after washing for 30 minutes at 65° C. at a low ion concentration [for example using 0.1×SSC (15 mM sodium chloride, 1.5 mM sodium citrate)].

The transcription regulating ability in the invention can be evaluated for example based on the assay employing a reporter gene described below.

First, a transformant is produced by introducing into a host cell a reporter gene connected to the downstream of a transcription controlling DNA containing a DNA region (5′-ACGTG-3′, SEQ ID No.16; hereinafter sometimes referred to as a present responsive DNA region) to which a transcription inhibiting complex of a Sim2 as a transcription regulatory factor and a present transcription coupling factor can be bound and a gene comprising a nucleotide sequence encoding the amino acid sequence of a test transcription regulatory factor, and then the expression level of the reporter gene possessed by the transformant or an index value correlating with the level is measured, and then based on the expression level or the index value correlating with the level thus measured the transcription regulating ability possessed by the test transcription regulatory factor to be tested is evaluated.

The transcription regulating ability described above may for example be an ability of promoting or inhibiting the transcription of a gene (which means a reporter gene in the case of an assay employing a reporter gene described above) located downstream of the DNA region.

A reporter gene in an evaluation method described above may for example be a luciferase gene, secretor alkaline phosphatase gene, β-galactosidase gene, chloramphenicol acetyl transferase gene, growth factor gene and the like, with a gene encoding a reporter protein which is relatively stable in a host cell being preferred.

First, a transformant is obtained by introducing a reporter gene connected to the downstream of a transcription controlling region containing a present ARNT family transcription coupling factor and a present responsive DNA region and a gene comprising a nucleotide sequence encoding the amino acid sequence of a test transcription regulatory factor (hereinafter sometimes referred to as a test transcription regulatory factor gene) into a host cell (for example, HeLa Cell, CV-1 cell, Hepa1 cell, NIH3T3 cell, HepG2 cell COS1 cell, BF-2 cell, CHH-1 cell and the like). In this procedure, the test transcription regulatory factor gene as being integrated into a basic vector operably connected to a promoter which is functional in the host cell may be introduced into the host cell. The reporter gene connected to the downstream of a transcription controlling region containing the present responsive DNA region may also be employed as being integrated into the basic vector. It is also possible that a vector into which a reporter gene connected to the downstream of a transcription controlling region containing a present responsive DNA region has been integrated and a vector comprising a test transcription regulatory factor gene operably connected to a promoter which is functional in a host cell may be introduced into the host cell together with a vector comprising a marker gene. Then, the cell is incubated usually for several weeks, and then the intended transformant is selected based on the expression level of the introduced marker gene, whereby obtaining a transformant yielding by introducing into the host cell the reporter gene connected to the downstream of the transcription controlling region containing the present responsive DNA region and the test transcription regulatory factor gene operably connected to the promoter which is functional in the host cell.

As used herein, the “promoter which is functional in the host cell” may for example be an inducible promoter such as a GAL1 promoter or a routinely expressed promoter such as an ADH promoter (the ADH1 promoter can be prepared by a standard genetic engineering method for example from an yeast expression vector pAAH5 comprising an ADH1 promoter and terminator [available from Washington Research Foundation, Ammerer et al., Method in Enzymology, 110 part (p. 192-201)]; the ADH1 promoter is encompassed in the U.S. patent application Ser. No. 299,733 by Washington Research Foundation, and should be used industrially or commercially in United States only after obtaining the approval from the claimant) when a host cell is a budding yeast cell. When the host cell is an animal cell, then a Rous sarcoma virus (RSV) promoter and cytomegalovirus (CMV) promoter may be mentioned. The transcription controlling region may for example be a DNA consisting of a minimum TATA box sequence derived from a gene capable of being expressed in a host cell, which is the minimum promoter which is capable of functioning in the host cell, typically a DNA comprising a TATA box and a nucleotide sequence consisting of about 50 nucleotides near the transcription initiation point.

A transformant thus prepared may be cultured for example for several hours to several days, and then the expression level of the reporter gene possessed by the transformant or an index value correlating with the level is measured. When the test transcription regulatory factor is activated by the present responsive DNA region, then the transcription of the reporter gene is promoted, and the reporter protein encoded by this reporter gene is accumulated in the cell of the transformant or secreted into the culture medium. By measuring the expression level of this reporter gene or the index value correlating with the level, the expression level of the reporter gene or the index value correlating with the level per cell of the transformant is measured. Typically, when a luciferase gene is employed as a reporter gene, a crude cell extract prepared from the transformant is combined with luciferrin which is a substrate for the luciferase, whereby allowing a luminescence to be emitted at an intensity in proportion with the luciferase level in this crude cell extract. Accordingly, by measuring this luminescence using a measuring device such as a luminometer, the luciferase level, and thus the luciferase gene expression level, can be determined. Similarly, the expression level of the reporter gene or an index value correlating with the level in a transformant (i.e., a control transformant) which contains the reporter gene connected to the downstream of the transcription controlling region containing the present responsive DNA region but does not contain the test transcription regulatory factor gene is measured and this measured value is compared with the expression level of the reporter gene or the index value correlating with the level described above, whereby evaluating the transcription regulating ability possessed by the test transcription regulatory factor gene.

An inventive transcription activating complex can be obtained by culturing an inventive transformant and then recovering the product, which is (1) an inventive transcription activating complex or (2) a present ARNT family transcription coupling factor plus a present transcription activating factor, from the culture, while many cases utilize the inventive transcription activating complex in the form of a transformant which expresses the inventive transcription activating complex.

An inventive transcription activating complex can be produced by introducing one or more vectors (i.e., present vectors) having an ability of producing an inventive transcription activating complex into a host cell. Typically, a single vector comprising the both of the DNAs, namely, (1) the DNA comprising a nucleotide sequence encoding the amino acid sequence of the transcription coupling factor of any of ARNT 1 to 3 and (2) the DNA comprising a nucleotide sequence encoding a present amino acid sequence simultaneously, or several vectors comprising such DNAs independently may be introduced into a host cell.

Any conventional introducing process may be used to introduce present vectors into a host cell depending on the host cell. For the introduction into an E. coli host cell, any conventional method may be used, for example, including calcium chloride method and electroporation method as disclosed in the text (J. Sambrook, E. F. Frisch, and T. Maniatis, Molecular Cloning 2nd edition, Cold Spring Harbor Laboratory Press, 1989). The introduction of the vector into a mammal host cell or an insect host cell may be performed according to any general gene transfection method such as calcium phosphate method, DEAE dextran method, electroporation method, and lipofection method. For the introduction into an yeast host cell, for example, Yeast transformation kit (Clontech) may be used based on lithium method.

The introduction of the viral genome into the host cell via the viral vector can be made not only by any of the above general gene transfection methods but also by infecting the host cell with viral particles which carry viral genome containing the both of the DNAs described above.

In order to select an inventive transformant, for example, a marker gene may be introduced into a host cell together with a present vector, and then the host cell may be cultured by any method depending on the characteristic of the marker gene. For example, the marker gene may be a drug resistance gene against a selection drug that has killing activity on the host cell, and the present vector-containing host cell may be cultured in a medium that contains the selection drug. Examples of the combination of the drug resistance gene and the selection drug include the combinations of a neomycin resistance gene and neomycin, a hygromycin resistance gene and hygromycin, and a blasticidin S resistance gene and blasticidin S. Alternatively, the marker gene may complement auxotrophy of the host cell, and the present vector-containing cell may be cultured in a minimal medium free of the nutrient concerning the auxotrophy. When the present vector is introduced into a host cell capable of expressing the both of the DNAs described above, DNA binding activity may be detected.

For example, the inventive transformant in which the both of the DNAs described above are located in the chromosome of the host cell is obtained as follows. The present vector and the marker-containing vector are each digested with a restriction enzyme or the like into a linear chain and then introduced into the host cell by any method as described above. The cell is cultured generally for several weeks and then selected based on the expression amount of the introduced marker gene to give a desired transformant. For example, the present vector which contains the drug resistance gene as the marker gene is introduced into the host cell by any method as described above. The cell is subcultured in a selection drug-containing medium for at least several weeks, and then the drug-resistant clone surviving in the form of a colony is subjected to pure culture, resulting in the inventive transformant in which the both of the DNAs described above are incorporated in the chromosome of the host cell. In order to confirm the incorporation of the inventive gene in the host cell chromosome, the genome DNA may be prepared from the cell by a conventional genetic engineering method, and then the both of the DNAs described above may be detected in the prepared genome DNA by PCR, Southern hybridization, or the like using a DNA comprising a partial nucleotide sequence of the introduced DNAs described above as a primer or a probe. The transformant can be stored in a frozen state and then allowed to awake as needed. Therefore, not every experiment needs the transformant preparation, and tests can be performed using the transformant with the characteristics and the handling conditions checked in advance.

By culturing the inventive transformant thus obtained and then recovering the product, which is (1) an inventive transcription activating complex or (2) a present ARNT family transcription coupling factor and a present transcription activating factor, from the culture, whereby producing an inventive transcription activating complex.

For example, the inventive transformant is a microorganism, and in such a case, the transformant may be cultured using any medium that appropriately contains any carbon source, any nitrogen source, any organic or inorganic salt, and the like each for general microorganism culture. The cultivation may be carried out according to any conventional method for general microorganisms, such as solid culture method and liquid culture method (such as rotary shaking culture, reciprocal shaking culture, jar fermenter culture, and tank culture). The culture temperature and the pH of the medium can be each selected from a certain range in which the microorganism can grow. For example, the culture is generally performed at a temperature of about 15° C. to about 40° C. at a pH of about 6 to about 8. The culture time period depends on various culture conditions but is generally from about one day to about five days. When the expression vector contains an inducible promoter such as a temperature-inducible promoter and an IPTG-inducible promoter, the induction time is preferably within one day and generally several hours.

On the other hand, the transformant may be an animal cell such as a mammal cell and an insect cell, and the transformant may be cultured using any medium for general cell culture. If the transformant is prepared using the selection drug, the culture is preferably performed in the presence of the selection drug. For example, the mammal cell may be cultured using a DMEM medium (Nissui) containing FBS at a final content of 10% at 37° C. under 5% CO2 while the medium may be replaced with fresh one every several days. After the cells are grown in a confluent state, for example, an about 0.25% (w/v) trypsin-containing PBS solution is added so that the cells are separated and dispersed. The cells are then diluted several times and inoculated into a new plate and further cultured. Similarly, the insect cell may be cultured using any insect cell culture medium such as a 10% (v/v) FBS and 2% (w/v) Yeastlate-containig Grace's medium at a culture temperature of 25° C. to 35° C. If the cell tends to peel off the plate as in the case of Sf21 cell, the cells may be dispersed by pipetting and subcultured without using the trypsin solution. When the transformant contains the virus vector such as baculovirus, the culture is preferably terminated before the cell is killed and the cytoplasmic effect is observed, for example, up to 72 hours after the viral infection.

The product, which is (1) an inventive transcription activating complex or (2) a present ARNT family transcription coupling factor and a present transcription activating factor, produced by the inventive transformant may be recovered from the culture by any appropriate combination of conventional isolation or purification processes. For example, after the culture is completed, the transformant cells are collected by centrifugation or the like, and the collected cells are suspended in a general buffer such as a buffer comprising 20 mM HEPES pH7, 1 mM EDTA, 1 mM DTT, and 0.5 mM PMSF and then homogenized in a Polytron, a ultrasonic apparatus, a Dounce homogenizer, or the like. The resulting homogenate may be ultracentrifuged at several tens thousand×g for several tens minutes to about one hour, and then the supernatant fraction may be taken to give a fraction containing (1) an inventive transcription activating complex or (2) a present ARNT family transcription coupling factor and a present transcription activating factor. In addition, the supernatant fraction may be subjected to any type of chromatography such as ion exchange, hydrophobic, gel filtration, or affinity chromatography to give (1) an inventive transcription activating complex or (2) a present ARNT family transcription coupling factor and a present transcription activating factor in a further purified state. In this process, the fraction containing the inventive transcription activating complex or the like may be identified by a DNA binding assay or the like using a probe of an oligonucleotide with a length of about 15 bp to about 200 bp including a present responsive DNA region.

The resulting inventive transcription activating complex may be used in a receptor binding assay or the like for evaluating the ability or the amount of any test substance to bind to or bound to the transcription activating complex.

A DNA (hereinafter sometimes referred to as a present transcription regulatory factor DNA) encoding a transcription regulatory factor comprising a present amino acid sequence (i.e., a present transcription regulatory factor), which forms an inventive transcription activating complex, may be obtained for example from a tissue of an animal such as human, mouse, rat and the like in accordance with a genetic engineering method described for example in J. Sambrook, E. F. Frisch, T. Maniatis, Molecular Cloning, 2nd Edition, Cold Spring Harbor Laboratory (1989).

Typically, a total RNA derived from a tissue of an animal such as human, mouse and rat is first prepared. For example, a brain tissue is pulverized in a solution containing a protein denaturant such as guanidine hydrochloride or guanidine thiocyanate, and then the pulverized material is treated with phenol, chloroform and the like, to denature the protein. The denatured protein is removed for example by a centrifugation to obtain a supernatant, from which the total RNA is extracted by a guanidine hydrochloride/phenol method, SDS-phenol method, guanidine thiocyanate/CsCl method and the like. A commercially available kit based on the methods described above may for example be ISOGEN (NIPPON GENE). The resultant total RNA is used as a template and an oligo dT primer is annealed to a poly A sequence of the RNA, whereby synthesizing a single-stranded cDNA using a reverse transcriptase. Then, the synthesized single-stranded cDNA is used as a template together with a primer which is an RNA obtained by inserting a nick and a gap into the RNA chain using an E. coli RnaseH, whereby synthesizing a double-stranded cDNA using an E. coli DNA polymerase I. Subsequently, the both ends of the synthesized double-stranded cDNA is made blunt using a T4 DNA polymerase. The double-stranded cDNA having both blunt ends is purified and recovered by means of a standard procedure such as a phenol-chloroform extraction and ethanol precipitation. A commercially available kit based on the methods described above may for example be a cDNA synthesis system plus (Amarsham Pharmacia Biotech) or a TimeSaver cDNA synthesis kit (Amarsham Pharmacia Biotech). Then the resultant double-stranded cDNA is ligated to a vector such as a plasmid pUC118 or phage lgt10 using a ligase to prepare a cDNA library. As such a cDNA library, a commercially available cDNA library (GIBCO-BPL or Clontech) may also be employed.

Alternatively, a genomic DNA may be prepared from a tissue sample of an animal such as human, mouse and rat in accordance with a standard method described for example in J. Sambrook, E. F. Frisch, T. Maniatis, Molecular Cloning, 2nd Edition, Cold Spring Harbor Laboratory (1989), or M. Muramatsu, “Labomanual genetic engineering” (Maruzen, 1988). For example, when the sample is a hair, 2 or 3 hairs are washed with a sterilized water and then with ethanol, cut into 2 to 3 mm pieces, which are combined with 200 ml of a BCL-Buffer [10 mM Tris-HCl (pH7.5), 5 mM MgCl2, 0.32 sucrose, 1 Triton X-100] followed by a Proteinase K at the final concentration of 100 ml/ml and SDS at the final concentration of 0.5 (w/v). The mixture thus obtained is incubated at 70° C. for 1 hour, and then subjected to a phenol/chloroform extraction to obtain a genomic DNA. When the sample is a peripheral blood, the sample is treated using a DNA-Extraction kit (Stratagene) and the like to obtain a genomic DNA. The resultant genomic DNA is ligated to a vector such as a lgt10 using a ligase to obtain a genomic DNA library. As such a genomic DNA library, a commercially available genomic DNA library (Stratagene) may also be employed.

From a cDNA library or genomic DNA library obtained as described above, an inventive DNA can be obtained for example by a polymerase chain reaction (hereinafter abbreviated as PCR) using as a primer an oligonucleotide comprising a partial nucleotide sequence of the nucleotide sequence represented by SEQ ID No.4, 5, 6 or 59 (or 60) or the nucleotide sequence complementary to said partial nucleotide sequence or by a hybridization method using as a probe a DNA comprising the nucleotide sequence represented by SEQ ID No.4, 5, 6 or 59 (or 60) or a partial nucleotide sequence of said partial nucleotide sequence.

A primer employed in a PCR may for example be an oligonucleotide having a length of about 10 nucleotides to about 50 nucleotides which is an oligonucleotide comprising a nucleotide sequence selected from a 5′ non-translation region of the nucleotide sequence represented by SEQ ID No.4, 5, 6 or 59 (or 60) and which is an oligonucleotide comprising the nucleotide sequence complementary to a nucleotide sequence selected from a 3′ non-translation region of the nucleotide sequence represented by SEQ ID No.4, 5, 6 or 59 (or 60). Typically, the forward primer may for example be the oligonucleotide consisting of the nucleotide sequence represented by SEQ ID NO.7 and the oligonucleotide consisting of the nucleotide sequence represented by SEQ ID NO.8. The reverse primer may for example be the oligonucleotide consisting of the nucleotide sequence represented by SEQ ID NO.9 and the oligonucleotide consisting of the nucleotide sequence represented by SEQ ID NO.10. An example of the PCR condition involves an incubation in 50 ml of a reaction solution containing 5 ml of a 10-fold diluted buffer for a LA-Taq polymerase (Takara), 5 ml of a 2.5 mM dNTP mixture (each 2.5 mM dATP, dGTP, dCTP and dTTP) (the final concentration of each of dATP, dGTP, dCTP and dTTP is 0.25 mM), each 0.25 to 1.25 ml of 20 mM primers (final concentration of 0.1 to 0.5 mM), 0.1 to 0.5 mg of a template cDNA and 1.25 units of a LA-Taq polymerase (Takara) for 1 minutes at 95° C. followed by 3 minutes at 68° C. in a single cycle, the cycle being repeated 35 times.

A probe employed in a hybridization method may for example be the DNA consisting of the nucleotide sequence represented by the nucleotide numbers 102 to 2507 in the nucleotide sequence represented by SEQ ID No.4, a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 51 to 2456 in the nucleotide sequence represented by SEQ ID No.5, a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 35 to 2440 in the nucleotide sequence represented by SEQ ID No.6, a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 1419 to 6164 in the nucleotide sequence represented by SEQ ID No.59 and the like. An example of the hybridization condition involves an incubation at 65° C. in the presence of 6×SSC (0.9M sodium chloride, 0.09M sodium citrate), 5× Denhart's solution (0.1 (w/v) ficoll 400, 0.1 (w/v) polyvinyl pyrrolidone), 0.1 (w/v) BSA), 0.5 (w/v) SDS and 100 mg/ml denatured salmon sperm DNA followed by an incubation at room temperature for 15 minutes in the presence of 1×SSC (0.15M sodium chloride, 0.015M sodium citrate) and 0.5 (w/v) SDS, followed by an incubation at 68° C. for 30 minutes in the presence of 0.1×SSC (0.015M sodium chloride, 0.0015M sodium citrate) and 0.5 (w/v) SDS. Alternatively, an incubation at 65° C. in the presence of 5×SSC, 50 mM HEPES, pH7.0, 10× Denhart's solution and 20 mg/ml denatured salmon sperm DNA followed by an incubation at room temperature for 30 minutes in 2×SSC, followed by an incubation at 65° C. for 40 minutes in 0.1×SSC, which is repeated twice, may also be exemplified.

A present transcription regulatory factor DNA can be prepared also by performing a chemical synthesis of a nucleic acid in accordance with a standard method such as a phosphite triester method (Hunkapiller, M. et al., Nature, 310, 105, 1984) based on the nucleotide sequence represented by SEQ ID NO.4, 5, 6 or 59 (or 60).

A present transcription regulatory factor DNA thus obtained can be cloned into a vector in accordance with a genetic engineering method described in J. Sambrook, E. F. Frisch, T. Maniatis, Molecular Cloning, 2nd Edition, Cold Spring Harbor Laboratory (1989). Typically, the cloning can for example be performed using a TA cloning kit (Invitrogen) or a commercially available plasmid vector such as pBluescriptII (Stratagene).

The nucleotide sequence of a resultant present transcription regulatory factor DNA can be identified by a Maxam Gilbert method (described for example in Maxam, A. M. & W. Glibert, Proc. Natl. Acad. Sci. USA, 74, 560, 1997) or a Sanger method (described for example in Sanger, F. & A. R. Coulson, J. Mol. Biol., 94, 441, 1975, Sanger, F. & Nicklen and A. R. Coulson., Proc. Natl. Acad. Sci. USA, 74, 5463, 1997).

A typical example of a present transcription regulatory factor DNA may for example be the DNA consisting of the nucleotide sequence represented by the nucleotide numbers 102 to 2507 in the nucleotide sequence represented by SEQ ID No.4, a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 51 to 2456 in the nucleotide sequence represented by SEQ ID No.5, a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 35 to 2440 in the nucleotide sequence represented by SEQ ID No.6, a DNA consisting of the nucleotide sequence represented by the nucleotide numbers 1419 to 6164 in the nucleotide sequence represented by SEQ ID No.59 and the like.

A present transcription regulatory factor DNA vector can be constructed by integrating a present transcription regulatory factor DNA, in accordance with a standard genetic engineering method, into a vector capable of being utilized in a host cell to which said gene is introduced (hereinafter referred to as a basic vector), such as a vector which contains a gene information capable of being replicated in the host cell, which can independently be proliferated, which can be isolated and purified from the host cell and which has a detectable marker.

A basic vector which can be employed for constructing a present transcription regulatory factor DNA vector may for example be a plasmid pUC119 (Takara) or phagimid pBluescriptII (Stratagene) when using a coliform as a host cell. When using a budding yeast as a host cell, then plasmids pGBT9, pGAD242, pACT2 (Clontech) may be exemplified. When using a mammalian cell as a host cell, a vector containing an autonomous replication origin derived from a virus such as pRc/RSV, pRc/CMV (Invitrogen), bovine papilloma virus plasmid pBV (Amarsham Pharmacia Biotech) or EB virus plasmid pCEP4 (Invitrogen) and a virus such as a vaccinia virus may be exemplified, while an insect virus such as a baculovirus may be exemplified when using a insect cell as a host cell. When the autonomous replication origin-containing vector such as the plasmid pACT2 for the yeast, the bovine papilloma virus plasmid pBPV, and the EB virus plasmid pCEP4 is used to form an inventive vector (or a present vector), the vector introduced in the host cell is held in the form of an episome in the cell.

In order to integrate a present transcription regulatory factor DNA into a virus such as a baculovirus or vaccinia virus, a transfer vector containing a nucleotide sequence homologous to the genome of a virus to be employed can be used. Such a transfer vector is typically a plasmid available from Pharmingen such as pVL1372, pVL1393 (Smith, G. E., Summers M. E. et al., Mol. Cell Biol., 3, 2156-2165 (1983) and pSFB5 (Funahashi, S. et al., J. Virol., 65, 5584-5588 (1991). When a present transcription regulatory factor DNA is inserted into a transfer vector described above and the transfer vector and the genome of a virus are introduced into a host cell simultaneously, a homologous recombination occurs between the transfer vector and the genome of the virus, whereby obtaining a virus into whose genome the present transcription regulatory factor DNA is integrated. The genome of a virus may be the genome for example of Baculovirus, Adenovirus, Vacciniavirus and the like.

More specifically, a present transcription regulatory factor DNA is integrated for example into a baculovirus by inserting the present transcription regulatory factor DNA into a multiple cloning site of a transfer vector such as pVL1393 or pBL1392 followed by introducing the DNA of said transfer vector and a baculovirus genome DNA (Baculogold; Pharmingen) into an insect cell line Sf21 (available from ATCC) for example by a calcium phosphate method followed by incubating the resulting cell. A virus particle containing the genome of the virus into which the present transcription regulatory factor DNA has been inserted is recovered from the culture medium for example by a centrifugation, and then made free from proteins using phenol and the like, whereby obtaining the genome of the virus containing the present transcription regulatory factor DNA. Subsequently, the genome of said virus is introduced into a host cell having a virus particle forming ability such as an insect cell line Sf21 for example by a calcium phosphate method and the resultant cell is incubated, whereby proliferating the virus particle containing the present transcription regulatory factor DNA.

On the other hand, a relatively small genome such as that of a mouse leukemia retrovirus can directly be integrated with a present transcription regulatory factor DNA without using any transfer vector. For example, a virus vector DC(X) (Eli Gilboa et al., BioTechniques, 4, 504-512 (1986)) is integrated with a present transcription regulatory factor DNA on its cloning site. The resultant virus vector into which the present transcription regulatory factor DNA has been integrated is introduced into a packaging cell such as an Ampli-GPE (J. Virol., 66, 3755 (1992)), whereby obtaining a virus particle containing the genome of the virus into which the present transcription regulatory factor DNA has been inserted.

A promoter capable of functioning in a host cell is operably connected to the upstream of a present transcription regulatory factor DNA and then integrated into a basic vector such as those described above, whereby constructing a present transcription regulatory factor DNA capable of allowing the present transcription regulatory factor DNA to be expressed in the host cell. The expression “operably connected” means that a promoter and a present transcription regulatory factor DNA are connected to each other in a condition which allows the present transcription regulatory factor DNA is expressed under the control of the promoter in a host cell into which the present transcription regulatory factor DNA is to be introduced. A promoter capable of functioning in a host cell may for example be a DNA exhibiting a promoter activity in a host cell into which it is to be introduced. Those which may be exemplified when the host cell is a coliform cell are E. coli lactose operon promoter (lacP), tryptophan operon promoter (trpP), arginine operon promoter (argP), galactose operon promoter (galP), tac promoter, T7 promoter, T3 promoter, λ phage promoter (λ-pL, λ-pR) and the like, while those which may be exemplified when the host cell is an animal cell or fission yeast are Rous sarcoma virus (RSV) promoter, cytomegalovirus (CMV) promoter, simian virus (SV40) early or late promoter, mouse mammary tumor virus (MMTV) promoter and the like. Those which may be exemplified when the host cell is a budding yeast are an ADH1 promoter and the like.

When a basic vector which initially possesses a promoter capable of functioning in a host cell is employed, a present transcription regulatory factor DNA may be inserted to the downstream of said promoter so that the vector-possessed promoter and the present transcription regulatory factor DNA are operably connected to each other. For example, each of the plasmids such as pRc/RSV and pRc/CMV described above is provided with a cloning site downstream of a promoter capable of functioning in an animal cell, and by inserting a present transcription regulatory factor DNA into said cloning site followed by a introduction into an animal cell, the present transcription regulatory factor DNA can be expressed. Since any of these plasmids has previously been integrated with a SV40 autonomous replication origin, the introduction of said plasmid into a host cell which has been transformed with an SV40 genome from which an ori is deleted, such as a COS cell, leads to an extremely increased number of the intracellular plasmid copies, resulting in a high expression of the present transcription regulatory factor DNA which has been integrated into said plasmid. Also since the plasmid pACT2 for yeast described above possesses an ADH1 promoter, a present transcription regulatory factor DNA vector capable of allowing a present transcription regulatory factor DNA to be expressed highly in a budding yeast such as CG1945 (Clontech) can be constructed by inserting the present transcription regulatory factor DNA into the downstream of the ADH1 promoter of said plasmid or a derivative thereof.

On the other hand, a vector comprising a DNA (hereinafter sometimes referred to as a present ARNT family transcription coupling factor DNA) comprising a nucleotide sequence encoding the amino acid sequence of any of ARNT1 to 3 can be produced by a method similar basically to the method for producing a present transcription regulatory factor DNA describe above except for using the present ARNT family transcription coupling factor DNA instead of the present transcription regulatory factor DNA. In this procedure, the present ARNT family transcription coupling factor DNA can be produced for example by designing a PCR primer pair for a Long PCR comprising the partial nucleotide sequences of the 5′ non-translation region and the 3′ non-translation region with referring to the nucleotide sequences such as human ARNT1 (accession No. NM_(—)001668), human ARNT2 (accession No. AB002305), human ARNT3 (accession No. D89722) disclosed in a database, followed by a PCR for amplifying, from a human Brain cDNA library, a DNA comprising a full length translation region within the present ARNT family transcription coupling factor gene which is a region of the gene sandwiched between the primer pair.

For producing a single vector simultaneously comprising the both of the DNAs, namely, (1) the DNA comprising a nucleotide sequence encoding the amino acid sequence of the transcription coupling factor of any of ARNT 1 to 3 (i.e., the present ARNT family transcription coupling factor DNA) and (2) the DNA comprising a nucleotide sequence encoding a present amino acid sequence (i.e., the present transcription regulatory factor DNA), the DNA comprising a nucleotide sequence encoding the amino acid sequence of the transcription coupling factor of any of ARNT 1 to 3 and the DNA comprising a nucleotide sequence encoding a present amino acid sequence are integrated simultaneously into an expression vector intended to integrate two genes into an identical plasmid and to express the genes simultaneously, such as a pBI vector (Clontech). It is also possible to produce several vectors comprising both DNAs independently for example by integrating the DNA comprising a nucleotide sequence encoding the amino acid sequence of the transcription coupling factor of any of ARNT 1 to 3 and the DNA comprising a nucleotide sequence encoding a present amino acid sequence independently into several ordinary expression vectors such as a pRC/RSV vector (Invitrogen).

A single vector comprising the both of the DNAs described above or several vectors comprising such DNAs independently can be employed as a Down's syndrome improving pharmaceutical.

An inventive transformant thus produced may be a transformant which contains the DNA of a reporter gene comprising a promoter operably connected thereto which is capable of being activated by an inventive transcription activating complex in addition to a present vector.

Such a transformant can be utilized for example in evaluating a substance for the ability of regulating the transcription promoting ability possessed by an inventive transcription activating complex. For example, a method for evaluating the present regulating ability possessed by a substance may for example be an evaluation method (i.e., an inventive evaluation method) which comprises the steps:

(1) a first step for bringing a test substance into contact with a transformant described above;

(2) a second step, after the first step, for measuring the expression level of the reporter gene possessed by the transformant or an index value correlating with the level; and,

(3) a third step for evaluating the substance for its ability of regulating the transcription promoting ability possessed by the transcription activating complex based on the expression level or the index value correlating with the level measured in the second step.

A further application is possible for example to a searching method (i.e., an inventive searching method) comprising a step for selecting a substance having an ability of regulating the transcription promoting ability possessed by the transcription activating complex based on a regulating ability evaluated by the evaluation method and a therapeutic agent (i.e., an inventive therapeutic agent), such as a Down's syndrome improving agent, containing as an active ingredient a substance searched for by such a searching method or a pharmaceutically acceptable salt thereof.

A therapeutic agent (i.e., an inventive therapeutic agent) containing as an active ingredient a substance selected by an inventive searching method or a pharmaceutically acceptable salt thereof can be administered at an effective dose orally or parenterally to a mammalian animal such as human. For example, the inventive therapeutic agent when administered orally can be given in an ordinary form such as a tablet, capsule, syrup and suspension. When the inventive therapeutic agent is given parenterally, it can be administered in an ordinary liquid form such as a solution, emulsion and suspension. A method for administering the inventive therapeutic agent in a form described above parenterally may for example be an injection or a rectal administration of a suppository.

Such a suitable dosage form can be produced by incorporating a substance selected by an inventive searching method or a pharmaceutically acceptable salt thereof into a pharmaceutically acceptable ordinary carrier, excipient, binder, stabilizer, diluent and the like. When employing an injection formulation, it may be possible to add acceptable buffering agents, solubilizing aids, osmotic agents and the like.

The dosage may vary depending on the age and the sex of the mammalian subject, degree of the disease, the type of the inventive therapeutic agent, dosage form and the like, the oral dose is usually about 1 mg to about 2 g as an active ingredient per day in an adult, preferably about 5 mg to about 1 g, while the injection may be given at about 0.1 mg to about 500 mg as an active ingredient in an adult. Such a daily dose may be given all at once or in several portions.

The invention also provides a transcription activating complex or transformant for a two-hybrid assay employing a region required for exerting the transcription promoting ability possessed by an inventive transcription activating complex.

Thus, the invention encompasses (1) an invention relating to a use of an inventive transcription activating complex and an inventive transcription activating complex 2 for a two-hybrid assay, and (2) an invention relating to a use of an inventive transformant and an inventive transformant 2 for a two-hybrid assay. For producing a system for such a two-hybrid assay, a commercial kit, such as Matchmaker Two-hybrid system (Clontech), CheckMate Mammalian Two-Hybrid System (Promega) may be employed.

An inventive transcription activating complex 2 contains a protein comprising one member (A or B) among the member I shown below and one member (X or Y) among the member II shown below and a protein comprising the other member (B or A) among the member I shown below and the other member (Y or X) among the member II shown below, and is a complex formed from the both proteins. It may also be a complex of the both proteins formed under the control by a ligand.

<<Member I>>

(A) A region to which a transcription regulatory factor comprising the present amino acid sequences is bound in the present ARNT family transcription coupling factor; or,

(B) A region to which the present ARNT family transcription coupling factor is bound in a transcription regulatory factor comprising the present amino acid sequence.

<<Member II>>

(X) A DNA binding region of a transcription regulatory factor which is functional in a host cell; or,

(Y) A transcription activating region of a transcription regulatory factor which is functional in a host cell.

In the invention, a transcription coupling factor comprising (A) in the member I is a transcription coupling factor which recognizes and thus binds to a complex of a present amino acid sequence-carrying transcription regulatory factor with a ligand, and also is a present ARNT family transcription coupling factor.

On the other hand, a transcription regulatory factor comprising (B) in the member I is a transcription regulatory factor comprising a present amino acid sequence which is capable of binding to a transcription coupling factor described above. In such a case, for the purpose of forming a complex with a ligand, the transcription regulatory factor has a region to which the ligand is bound. A DNA comprising a nucleotide sequence encoding the amino acid sequence of such a region is a partial nucleotide sequence of the transcription regulatory factor, such as the nucleotide sequence represented by the nucleotide numbers 132 to 2507 in the nucleotide sequence represented by SEQ ID No.4.

A transcription regulatory factor comprising (X) in the member II may for example be a transcription regulatory factor which binds to a DNA consisting of any of the nucleotide sequence such as the nucleotide sequence of the DNA to which a Gal4 protein is bound (5′-CGGAGGACTGTCCTCCG-3′, SEQ ID No.11), the nucleotide sequence of the DNA to which a Lex protein is bound (5′-TACTGTATGTACATACAGTA-3′, SEQ ID No.12), the nucleotide sequence of the DNA to which a Lac I receptor protein is bound (5′-GAATTGTGAGCGCGCACAATTC-3′, SEQ ID No.13), the nucleotide sequence of the DNA to which a tetracyclin receptor protein is bound (5′-TCGAGTTTACCACTCCCTATCAGTGATAGAGAAAAGTGAAAG-3′, SEQ ID No.14), the nucleotide sequence of the DNA to which a ZFHD-1 protein is bound (5′-TAATGATGGGCG-3′, SEQ ID No.15), the nucleotide sequence of the DNA to which a transcription inhibiting complex of the transcription coupling factor of any of ARNT 1 to 3 with the Sim2 as a transcription regulatory factor can be bound (5′-ACGTG-3′, SEQ ID No.16), and also is a transcription regulating factor which is functional in a host cell. On the other hand, a transcription regulatory factor comprising (Y) in the member II may for example be a transcription regulatory factor capable of functioning in a host cell such as a Gal4 protein, Lex protein, Lac I receptor protein; tetracyclin receptor protein, ZFHD-1 protein, B42 protein, a protein as a present ARNT transcription coupling factor and VP16 protein.

A transcription activating complex consisting of such various member is produced for example by an inventive transformant 2.

With regard to an inventive transformant 2, (a) in the member i means a DNA comprising a nucleotide sequence encoding the amino acid sequence of (A) in the member I, and such a DNA can be prepared by an ordinary genetic engineering method from a gene of a transcription coupling factor comprising (A) in the member I. On the other hand, (b) in the member i means a DNA comprising a nucleotide sequence encoding the amino acid sequence of (B) in the member I, and such a DNA can be prepared by an ordinary genetic engineering method from a gene of a present transcription regulatory factor comprising (B) in the member I.

(x) in the member ii means a DNA comprising a nucleotide sequence encoding the amino acid sequence of (X) in the member II, and such a DNA can be prepared by an ordinary genetic engineering method from a gene of a transcription coupling factor comprising (A) in the member I. On the other hand, (y) in the member ii means a DNA comprising a nucleotide sequence encoding the amino acid sequence of (Y) in the member II, and such a DNA can be prepared by an ordinary genetic engineering method from a gene of a present transcription regulatory factor comprising (Y) in the member II.

The member iii means a DNA comprising a reporter gene connected to the downstream of a promoter containing a DNA to which (X) in the member II can be bound. As used herein, a reporter gene means a reporter gene employed in an ordinary reporter assay such as a luciferase gene, secretor alkaline phosphatase gene, β-galactosidase gene, chloramphenicol acetyl transferase gene, growth factor gene and the like, with gene encoding a reporter protein which is relatively stable in a host cell being preferred. A DNA to which (X) in the member II can be bound may for example be a DNA consisting of any of the nucleotide sequences such as the nucleotide sequence of the DNA to which a Gal4 protein is bound (5′-CGGAGGACTGTCCTCCG-3′, SEQ ID No.11), the nucleotide sequence of the DNA to which a Lex protein is bound (5′-TACTGTATGTACATACAGTA-3′, SEQ ID No.12), the nucleotide sequence of the DNA to which a Lac I receptor protein is bound (5′-GAATTGTGAGCGCGCACAATTC-3′, SEQ ID No.13), the nucleotide sequence of the DNA to which a tetracyclin receptor protein is bound (5′-TCGAGTTTACCACTCCCTATCAGTGATAGAGAAAAGTGAAAG-3′, SEQ ID No.14), the nucleotide sequence of the DNA to which a ZFHD-1 protein is bound (5′-TAATGATGGGCG-3′, SEQ ID No.15), the nucleotide sequence of the DNA to which a transcription inhibiting complex of the transcription coupling factor of any of ARNT 1 to 3 with the Sim2 as a transcription regulatory factor can be bound (5′-ACGTG-3′, SEQ ID No.16).

Each of such various members is combined with each other as appropriate for the expression of an inventive transcription regulatory factor 2 and inserted into a vector, which is then introduced into an identical host cell using an ordinary genetic engineering method, whereby obtaining a present transformant. In such a case, each member may be introduced into an identical host cell (1) in the state where the member iii is kept independent, or (2) in the state where two chimera genes, namely, a chimera gene 1 obtained by ligating one member (a or b) among the member i and one member (x or y) among the member ii with aligning their nucleotide sequence reading frame and a chimera gene 2 obtained by ligating the other member (b or a) among the member i and the other member (y or x) among the member ii with aligning their nucleotide sequence reading frame, are produced and each of these chimera genes 1 and 2 is connected to the downstream of the promoter which is functional in the host cell (such as an inducible promoter such as a GAL1 promoter or a routinely expressed promoter such as an ADH promoter when a host cell is a budding yeast cell). When a utilizable intrinsic reporter gene is possessed by a host cell, then it may be utilized, and in such a case the introduction of a reporter gene can be omitted.

A host cell used for producing an inventive transformant 2 may for example be a budding yeast cell, a mammalian cell such as HeLa cell.

In a present evaluation method, a transformant and a test substance are allowed to be in contact with each other for several hours to several days, typically a transformant is cultured in a medium supplemented with a test substance for several hours to several days, and then the expression level of the reporter gene possessed by the transformant or an index value correlating with the level is measured. When the present transcription activating complex produced by the transformant is activated as a result of the binding of the test substance, the transcription of the reporter gene is promoted, and the reporter protein encoded by this reporter gene is accumulated in the cell of the transformant or secreted into the culture medium. By measuring the expression level of this reporter gene or the index value correlating with the level, the expression level of the reporter gene or the index value correlating with the level per cell of the transformant is measured.

Typically, when a luciferase gene is employed as a reporter gene, a crude cell extract prepared from the transformant which has been brought into contact with a test substance is combined with luciferrin which is a substrate for the luciferase, whereby allowing a luminescence to be emitted at an intensity in proportion with the luciferase level in this crude cell extract. Accordingly, by measuring this luminescence using a measuring device such as a luminometer, the luciferase level, and thus the luciferase gene expression level, can be determined. Similarly, the expression level of the reporter gene or an index value correlating with the level under the conditions involving no contact between the transformant and the test substance is measured, and this measured value is compared with the expression level of the reporter gene or an index value correlating with the level under the conditions involving the contact with the test substance, whereby evaluating the present regulating ability possessed by the test substance.

Based on a present regulating ability evaluated by an evaluation method described above, a substance having the present regulating ability can readily be selected, and a therapeutic agent containing such a substance or a pharmaceutically acceptable salt thereof as an active ingredient can be provided.

A therapeutic agent (i.e., an inventive therapeutic agent) containing as an active ingredient a substance selected by an inventive searching method or a pharmaceutically acceptable salt thereof can be administered at an effective dose orally or parenterally to a mammalian animal such as human. For example, the inventive therapeutic agent when administered orally can be given in an ordinary form such as a tablet, capsule, syrup and suspension. When the inventive therapeutic agent is given parenterally, it can be administered in an ordinary liquid form such as a solution, emulsion and suspension. A method for administering the inventive therapeutic agent in a form described above parenterally may for example be an injection or a rectal administration of a suppository.

Such a suitable dosage form can be produced by incorporating a substance selected by an inventive searching method or a pharmaceutically acceptable salt thereof into a pharmaceutically acceptable ordinary carrier, excipient, binder, stabilizer, diluent and the like. When employing an injection formulation, it may be possible to add acceptable buffering agents, solubilizing aids, osmotic agents and the like.

The dosage may vary depending on the age and the sex of the mammalian subject, degree of the disease, the type of the inventive therapeutic agent, dosage form and the like, the oral dose is usually about 1 mg to about 2 g as an active ingredient per day in an adult, preferably about 5 mg to about 1 g, while the injection may be given at about 0.1 mg to about 500 mg as an active ingredient in an adult. Such a daily dose may be given all at once or in several portions.

A disease for which an inventive therapeutic agent is indicated may for example be a disease related to Down's syndrome such as mental retardation.

The present invention is also directed to a receptor binding assay (the inventive binding assay).

The inventive binding assay enables the measurement of the ability of any chemical substance to bind to the inventive transcription activating complex 2, the quantification of the binding amount, and the analysis of the binding specificity or the binding strength. For example, a labeled ligand is preliminarily allowed to bind to the inventive transcription activating complex 2, which is recovered from the inventive transformant 2 as described above. The test material is then allowed to coexist with the labeled ligand so that the test substance competes with the labeled ligand. Depending on the affinity of each for the inventive transcription activating complex 2, the labeled ligand is released from the complex. The amount of the labeled ligand bound to the complex decreases, and therefore, the amount of the label bound to the complex decreases. Thus, the label amount of the free form or the bound form of the labeled ligand may be monitored to indirectly determine the binding state between the inventive transcription activating complex 2 and the test substance. For example, such a process enables the measurement of the ability of the test substance to bind to the inventive transcription activating complex 2.

The bound and free forms of the labeled ligand may be separated by hydroxyapatite method, glycerol density gradient ultracentrifugation or the like. The reaction system may broadly be classified into three groups. The first group includes a system in which only a solvent is added to the labeled ligand-bound inventive transcription activating complex 2 and corresponds to the system in which the addition amount of the test substance is zero. In this system, the label amount of the bound form of the labeled ligand represents the total amount of the labeled ligand bound to the inventive transcription activating complex 2 (the total binding amount). The second group includes a system in which for example, an unlabeled ligand is added to the labeled ligand-bound inventive transcription activating complex 2 in such a concentration that the inventive transcription activating complex 2 is saturated with the unlabeled ligand so as to have no capacity for binding to the labeled ligand (for example, 10 mM). In this system, the label amount of the bound form of the labeled ligand is determined as the amount of the labeled ligand nonspecifically bound to the inventive transcription activating complex 2 (the nonspecific binding amount). Therefore, the amount of the labeled ligand specifically bound to the inventive transcription activating complex 2 (the specific binding amount) is calculated by subtracting the nonspecific binding amount from the total binding amount. The third group includes a system in which the test substance is added to the labeled ligand-bound inventive transcription activating complex 2 at a final concentration of 10 mM, for example (such a concentration may arbitrarily be altered depending on the purpose). If the test substance has the ability to bind to the inventive transcription activating complex 2, the label amount of the bound form of the labeled ligand obtained in this system will be smaller than the specific binding amount obtained as described above under the condition that the addition amount of the test material is zero. Thus, the binding state between the inventive transcription activating complex 2 and the test substance is indirectly determined. The inventive binding assay may be performed to determine the ability of the test substance to bind to the inventive transcription activating complex 2. If the test substance include different substances, the assay can also determine whether the test substance includes any substance that has an affinity for the inventive transcription activating complex 2. If the ability of the test substance to bind to the inventive transcription activating complex 2 should be evaluated in a more detailed manner, for example, the test substance may be added at different concentrations in the third group in the process of the inventive binding assay. For example, the label amount of the bound form of the labeled ligand may be determined to produce the amounts of the bound and free forms of the ligand, respectively, and then the results may be subjected to the Scatchard analysis so that the binding affinity, the binding specificity, the binding capacity, or the like can be evaluated between the test substance and the inventive transcription activating complex 2.

The invention relating to a reporter assay, the invention relating to a two-hybrid assay and the inventive binding assay can be utilized for detecting a substance as an active ingredient for example in a Down's syndrome improving agent.

EXAMPLES

The present invention is further described in the following Examples, which are not intended to restrict the invention.

Example 1 Preparation of Present Transcription Regulatory Factor (mNXF) and Preparation of pGEM-mNXF as Vector Containing the Same

Polynucleotides consisting of the nucleotide sequences represented by SEQ ID NOs.7 and 9 were synthesized using a DNA synthesizer (Applied Biosystems Model 394). Using the polynucleotides thus synthesized as primers together with a template which was 10 ng of a mouse Brain cDNA library (#10655-017, Gibco BRL), a PCR was conducted in which each 10 pmol of the polynucleotide described above was added to 50 μl of the reaction solution, and an LA-Taq polymerase (Takara) and a buffer attached to the kit containing this enzyme were employed. The reaction conditions of this PCR which employed a PCR system 9700 (Applied Biosystems) involved 35 cycles in total, each cycle consisting of an incubation for 1 minutes at 95° C. followed by 3 minutes at 68° C.

Then, the entire volume of the PCR reaction solution thus obtained was subjected to a low melting point agarose gel electrophoresis (agarose L, Nippon Gene) to purify and recover the amplified DNA fragment (about 2.5 kb). A part of the DNA thus purified and recovered was used together with a dye terminator sequence kit FS (Applied Biosystems) to prepare a direct sequencing sample, which was subjected to a direct nucleotide sequencing using an autosequencer (Applied Biosystems, Model 3700).

Subsequently, the amplified DNA (about 1 μg) purified and recovered as described above was mixed with a pGEM T easy vector (Promega) (10 ng), and combined with a T4 DNA Ligase to effect a reaction, whereby obtaining a pGEM-mNXF. The nucleotide sequence of the resultant pGEM-mNXF was determined using an ABI Model 3700 autosequencer by a dye terminator method. The determined nucleotide sequence was compared with the nucleotide sequence obtained by the direct sequencing described above, and it was confirmed that the nucleotide sequence in the translation region exhibited a complete agreement.

Example 2 Tests for Verifying Transcription Promoting Ability of the Inventive Transcription Activating Complex

(2-1) Preparation of pGL3-TATA-Galx4 (Construction of Reporter Gene Plasmid into Which 4 Copies of DNA Binding Region of GAL4 as Transcription Regulatory Factor has been Introduced into Upstream of Luciferase Gene Comprising TATA Minimum Promoter)

A pGL3-TATA-Galx4 reporter gene plasmid employed for measuring the transcription regulating ability of a chimera protein of the DNA binding region of GAL4 as a transcription regulatory factor and any optional transcription regulatory factor is one formed by introducing, into the upstream of the luciferase gene comprising a TATA minimum promoter, 4 copies in tandem of a DNA to which the GAL4 DNA binding region can be bound. By measuring the expression level of the luciferase in the case that the chimera protein of the GAL4 DNA binding region and any transcription regulatory factor exerts its effect on the reporter gene plasmid described above, the transcription regulation ability possessed by this chimera protein can advantageously be measured. This pGL3-TATA-Galx4 reporter gene plasmid was prepared as described below.

First, two oligonucleotides each comprising a DNA to which the GAL4 DNA binding region can be bound (SEQ ID No.17: 5′-cgcgtcgagctcgggtcggaggactgtcctccgactgctcgagtcgagctcgggtcggaggactgtcctccgactgctcgaga-3′, SEQ ID No.18:5′-cgcgtctcgagcagtcggaggacagtcctccgacccgagctcgactcgagcagtcggaggacagtcctccgacccgagctcga-3′) were hybridized, and phosphorylated at the 5′ terminal using a T4 kinase, and then connected in tandem using a T4 Ligase. The resultant double-stranded oligonucleotide was subjected to a low melting point agarose electrophoresis (NuseiveGTG; FMCbio) to recover a DNA fragment in which these double stranded oligonucleotide are connected in tandem. The DNA fragment thus recovered was used as an insert fragment. It was ligated with the pGL3-TATA vector (0.1 μg) which had been cleaved with MluI and then treated with an alkaline phosphatase (BAP C75; Takara) in the presence of a T4 Ligase (Takara) (reaction at 16° C. for 16 hours), whereby obtaining a pGL3-TATA-Galx4 (a reporter gene plasmid formed by introducing, into the upstream of the luciferase gene comprising a TATA minimum promoter, 4 copies of the DNA binding region of GAL4 as a transcription regulatory factor).

(2-2) pRC/RSV-Gal4-DBD Preparation (Construction of Plasmid Expressing DNA Binding Region of GAL4 as Transcription Regulatory Factor)

On the other hand, a pRC/RSV-Gal4-DBD which is a plasmid expressing only the DNA binding region of GAL4 as a transcription regulatory factor (hereinafter sometimes designated as Gal4-DBD, a part lacking the transcriptional control region of GAL4) was prepared as described below.

A pM which is a plasmid comprising a DNA encoding a Gal4-DBD (contained in a commercial kit K1602-1; Clontech) was cleaved with NheI and XbaI, and then made blunt-ended using a T4 polymerase. This was subjected to a low melting point agarose electrophoresis (agarose L: Nippon Gene) to recover a DNA fragment (about 500 bp) encoding a Gal4-DBD. The recovered DNA fragment was employed as an insert fragment.

Then, a pRC/RVS (Invitrogen) was cleaved with HindIII, and made blunt-ended using a T4 polymerase. This was BAP-treated and used as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase, whereby obtaining a pRC/RSV-Gal4-DBD). The correct construction of the plasmid for expressing the Gal4-DBD under the control of the RSV promoter was verified using an ABI Model 3700 autosequencer to determine the nucleotide sequence by a dye terminator method.

(2-3) pRC/RSV-MA, pRC/RSV-MB, pRC/RSV-MC Preparation

(construction of plasmid in which recognition site of pmaci as restriction enzyme giving blunt end in frame different from each other is introduced into downstream of DNA encoding Gal4-DBD for expressing chimera protein obtained by binding DNA binding region of GAL4 as transcription regulatory factor with transcription activating region of optional transcription regulatory factor)

While each of pRC/RSV-MA, pRC/RSV-MB, pRC/RSV-MC has a translation region of the Gal4-DBD downstream of the RSV promoter, and can be connected, at a further downstream PmaCI cleavage-derived blunt end, with a blunt-ended DNA fragment in such a manner that the translation frame of the DNA encoding the Gal4-DBD is in agreement with the translation frame of the blunt-ended DNA fragment. As a result, a chimera protein in which a GAL4 DNA binding region has been connected to a transcription regulation region of any optional transcription regulatory factor can be expressed.

Specifically, each of the pRC/RSV-MA, pRC/RSV-MB and pRC/RSV-MC was prepared as described below.

First, two oligonucleotides (SEQ ID No.19:5′-agcttcatcccacgtgagtcat-3′, SEQ ID No.20: 5′-ctagatgactcacgtgggatga-3′) were hybridized and then phosphorylated at the 5′ terminal using a T4 kinase. This was used as an insert fragment. On the other hand, the pRC/RSV-Gal4-DBD prepared in Section (2-2) described above was used as a vector after the cleavage with HindIII 29dand XbaI followed by the BAP treatment. The both were then ligated using a T4 Ligase, whereby obtaining a pRC/RSV-MA. Similarly, other two nucleotides (SEQ ID No.21: 5′-agcttcatccacacgtgagtcat-3′, SEQ ID No.22: 5′-ctagatgactcacgtgtggatga-3′) were hybridized and then phosphorylated at the 5′ terminal using a T4 kinase, and then was used as an insert fragment, whereby obtaining a pRC/RSV-MB. Similarly, other two nucleotides (SEQ ID No.23: 5′-agcttcatccaacacgtgagtcat-3′, SEQ ID No.24: 5′-ctagatgactcacgtgttggatga-3′) were hybridized and then phosphorylated at the 5′ terminal using a T4 kinase, and then was used as an insert fragment, whereby obtaining a pRC/RSV-MC.

(2-4) Preparation of pBlue-hArnt1kozac, pBlue-hArnt2kozac, pBlue-hArnt3kozac, pGEM-hBMAL2kozac, pRC/RSV-hSim2kozac and pBlue-hClockkozac (Construction of plasmids required for two-hybrid assay).

(2-4-1) pBlue-hArnt1kozac

pBlue-hArnt1kozac which is a plasmid comprising a full length Arnt1 translation region was prepared as described below.

First, from a human liver mRNA (purchased from Clontech), a single stranded cDNA was prepared using a polydT primer (purchased from Amersham Pharmacia) and a reverse transcriptase (SuperScriptII purchased from Gibco). The resultant cDNA was employed as a template together with the forward primer 5′-ggccatggcggcgactactgccaaccccgaaatga-3′ (SEQ ID No.25) and the reverse primer 5′-tgagggaagggaagggagaggaacttttattctgt-3′ (SEQ ID No.26) as well as a Pyrobest polymerase (Takara) to perform a PCR to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 3 minutes. The amplified DNA thus obtained fragment was subjected to a 500-fold dilution with TE and used as a template together with the forward primer 5′-cccggcggccgcccagccaccatggcggcgactactgccaaccccgaaatgacatc-3′ (SEQ ID No.27) and the reverse primer 5′-cccgtctagaaccccttatcctcaccccaatagttctattctgaa-3′ (SEQ ID No.28) as well as a Pyrobest polymerase (Takara) to perform a PCR again to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 3 minutes. The amplified DNA thus obtained fragment had a kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of a DNA encoding Arnt1 and a NotI restriction enzyme site further upstream thereof. Into the downstream of the stop codon possessed by this amplified DNA fragment, an XbaI restriction enzyme site was further introduced. The resultant amplified DNA fragment was cleaved with the both of the restriction enzymes NotI and XbaI and subjected to a low melting point agarose electrophoresis to purify and recover a DNA fragment. The purified and recovered DNA fragment was employed as an insert fragment.

Subsequently, a pBluescript vector which had been cleaved with NotI and XbaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pBlue-hArnt1kozac. The correct construction of this plasmid and the correct nucleotide sequence for the Arnt1-encoding DNA translation part were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-4-2) pBlue-hArnt2kozac

pBlue-hArnt2kozac which is a plasmid comprising a full length Arnt2-encoding DNA translation region was prepared as described below.

First, from a human Brain mRNA (purchased from Clontech) a single stranded cDNA was prepared using a polydT primer (purchased from Amersham Pharmacia) and a reverse transcriptase (SuperScriptII; purchased from Gibco). The resultant cDNA was employed as a template together with the forward primer 5′-catctctcacctggactgctgtgaccttcattcat-3′ (SEQ ID No.29) and the reverse primer 5′-cacatgggcatcgacatcacagtatgggtggcact-3′ (SEQ ID No.30) as well as a Pyrobest polymerase (Takara) to perform a PCR to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment was subjected to a 500-fold dilution with TE and used as a template together with the forward primer 5′-gggcgcggccgcccagccaccatggcttcagacatacctggatctgtgacgttgcc-3′ (SEQ ID No.31) and the reverse primer 5′-gggctctagactactcagaaaacggtggaaacatgcccaggtcgg-3′ (SEQ ID No.32) as well as a Pyrobest polymerase (Takara) to perform a PCR again to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment had a kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of a DNA encoding Arnt2 and a NotI restriction enzyme site further upstream thereof. Into the downstream of the Stop codon possessed by this amplified DNA fragment, an XbaI restriction enzyme site was further introduced. The resultant amplified DNA fragment was cleaved with the both of the restriction enzymes NotI and XbaI and subjected to a low melting point agarose electrophoresis to purify and recover a DNA fragment. The purified and recovered DNA fragment was employed as an insert fragment.

Subsequently, a pBluescript vector which had been cleaved with NotI and XbaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pBlue-hArnt2kozac. The correct construction of this plasmid and the correct nucleotide sequence for the Arnt2-encoding DNA translation part were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-4-3) pBlue-hArnt3kozac

pBlue-hArnt3kozac which is a plasmid comprising a full length Arnt3-encoding DNA translation region was prepared as described below.

First, from a human Brain mRNA (purchased from Clontech), a single stranded cDNA was prepared using a polydT primer (purchased from Amersham Pharmacia) and a reverse transcriptase (SuperScriptII; purchased from Gibco). The resultant cDNA was employed as a template together with the forward primer 5′-atggacacagacaaagatgaccctcatggaaggtt-3′ (SEQ ID No.33) and the reverse primer 5′-tgtttacagcggccatggcaagtcactaaagtcaac-3′ (SEQ ID No.34) as well as a Pyrobest polymerase (Takara) to perform a PCR to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment was subjected to a 500-fold dilution with TE and used as a template together with the forward primer 5′-ggggcggccgccccagccaccatggacacagacaaagatgaccctcatggaaggtt-3′ (SEQ ID No.35) and the reverse primer 5′-gggtctagatgtttacagcggccatggcaagtcactaaagtcaac-3′ (SEQ ID No.36) as well as a Pyrobest polymerase (Takara) to perform a PCR again to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment had a kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of a DNA encoding Arnt3 and a NotI restriction enzyme site further upstream thereof. Into the downstream of the stop codon possessed by this amplified DNA fragment, an XbaI restriction enzyme site was further introduced. The resultant amplified DNA fragment was cleaved with the both of the restriction enzymes NotI and XbaI and subjected to a low melting point agarose electrophoresis to purify and recover a DNA fragment. The purified and recovered DNA fragment was employed as an insert fragment.

Subsequently, a pBluescript vector which had been cleaved with NotI and XbaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pBlue-hArnt3kozac. The correct construction of this plasmid and the correct nucleotide sequence for the Arnt3-encoding DNA translation part were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-4-4) pGEM-hBmal2kozac

pGEM-hBmal2kozac which is a plasmid comprising a full length Bmal2-encoding DNA translation region was prepared as described below.

First, from a human Brain mRNA (purchased from Clontech), a single stranded cDNA was prepared using a polydT primer (purchased from Amersham Pharmacia) and a reverse transcriptase (SuperScriptII; purchased from Gibco). The resultant cDNA was employed as a template together with the forward primer 5′-agctatggggtcttccagctcacacatgacagag-3′ (SEQ ID No.37) and the reverse primer 5′-atcaaaggctagagggtccactggatgtcactgaa-3′ (SEQ ID No.38) as well as a Pyrobest polymerase (Takara) to perform a PCR to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment was subjected to a 500-fold dilution with TE and used as a template together with the forward primer 5′-gggcgcggccgcccagccaccatggggtcttccagctcacacatgacagagtttcc-3′ (SEQ ID No.39) and the reverse primer 5′-atcaaaggctagagggtccactggatgtcactgaa-3′ (SEQ ID No.40) as well as a LA-Taq polymerase (Takara) to perform a PCR again to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment had a kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of a DNA encoding Bmal2 and a NotI restriction enzyme site further upstream thereof. The resultant amplified DNA fragment was subjected to a low melting point agarose electrophoresis for the purification and the recovery. The amplified DNA thus purified and recovered was employed as an insert fragment. This insert fragment (0.5 μg) was ligated with a pGEMeasyT (purchased from Promega) vector (0.1 μg) using a T4 Ligase to yield pGEM-hBmal2kozac. The correct construction of this plasmid and the correct nucleotide sequence of the DNA encoding Bmal2 translation part were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-4-5) pRC/RSV-hSim2kozac

pRC/RSV-hSim2kozac which is a plasmid comprising a full length Sim2-encoding DNA translation region was prepared as described below.

First, from a human Kidney mRNA (purchased from Clontech), a single stranded cDNA was prepared using a polydT primer (purchased from Amersham Pharmacia) and a reverse transcriptase (SuperScriptII: purchased from Gibco). The resultant cDNA was employed as a template together with the forward primer 5′-gtctaatatgcccggagccgaggcgcgatgaagga-3′ (SEQ ID No.41) and the reverse primer 5′-tcacctcccgttggtgatgatgaccgaggcgcccag-3′ (SEQ ID No.42) as well as a Pyrobest polymerase (Takara) to perform a PCR to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DNA thus obtained fragment was subjected to a 500-fold dilution with TE and used as a template together with the forward primer 5′-gggcgcggccgcccagccaccatgaaggagaagtccaagaatgcggccaagaccag-3′ (SEQ ID No.43) and the reverse primer 5′-gggctctagatcacctcccgttggtgatgatgaccgaggcgccca-3′ (SEQ ID No.44) as well as a Pyrobest polymerase (Takara) to perform a PCR again to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 2 minutes. The amplified DMA thus obtained fragment had a kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of a DNA encoding Sim2 and a NotI restriction enzyme site further upstream thereof. Into the downstream of the Stop codon possessed by this amplified DNA fragment, an XbaI restriction enzyme site was further introduced. The resultant amplified DNA fragment was cleaved with the both of the restriction enzymes NotI and XbaI and subjected to a low melting point agarose electrophoresis to purify and recover a DNA fragment. The purified and recovered DNA fragment was employed as an insert fragment.

Subsequently, a pRC/RSV vector which had been cleaved with NotI and XbaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-hSim2kozac. The correct construction of this plasmid and the correct nucleotide sequence for the Sim2-encoding DNA translation part were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-4-6) pBlue-hClockkozac

pBlue-hClockkozac which is a plasmid comprising a full length Clock translation region was prepared as described below.

First, from a human Brain mRNA (purchased from Clontech), a single stranded cDNA was prepared using a polydT primer (purchased from Amersham Pharmacia) and a reverse transcriptase (SuperScriptII; purchased from Gibco). The resultant cDNA was employed as a template together with the forward primer 5′-gatccaaggagtacaaaaggagaagtacaaatgtc-3′ (SEQ ID No.45) and the reverse primer 5′-tactgcatctcatgaaactgctggaactttccct-3′ (SEQ ID No.46) as well as a Pyrobest polymerase (Takara) to perform a PCR to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 3 minutes. The terminal of the amplified DNA fragment thus obtained was phosphorylated using a T4 kinase, and then subjected to a low melting point agarose electrophoresis to purify and recover an amplified DNA fragment (about 2.5 kbp). The amplified DNA fragment thus purified and recovered was employed as an insert fragment. A pBluescript II vector (Stratagene) which had been cleaved with SmaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pBlue-hClock. The correct Clock translation sequence of the resultant plasmid were verified by investigating the all nucleotide sequence of the translation sequence part.

Subsequently, 1 μg of this plasmid was employed as a template together with the forward primer 5′-gggcgggatccccagccaccatgttgtttaccgtaagctg-3′ (SEQ ID No.47) and the reverse primer 5′-ctactgtggttgaaccttgg-31 (SEQ ID No.48) as well as a Pyrobest polymerase (Takara) to perform a PCR again to obtain an amplified DNA fragment. The PCR condition involved 35 cycle in total, each cycle being performed at 95° C. for 1 minutes followed by 68° C. for 3 minutes. The amplified DNA thus obtained has a kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of the Clock. The terminal of the amplified DNA fragment thus obtained was phosphorylated using a T4 kinase, and then subjected to a low melting point agarose electrophoresis for purification and recovery. The amplified DNA fragment thus purified and recovered was employed as an insert fragment described above. Then, a pBluescript II vector which had been cleaved with SmaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) using a T4 Ligase to prepare a pBlue-hClock kozac. The correct nucleotide sequence of the translation part of the DNA encoding the Clock in the plasmid thus prepared was verified by investigating the total nucleotide sequence of this translation part.

(2-5) Preparation of pRC/RSV-MC-mNXF(bHLH-PAS), pRC/RSV-MC-Arnt1 (bHLH-PAS), pRC/RSV-MC-Arnt2(bHLH-PAS), pRC/RSV-MB-Arnt3(bHLH-PAS), pRC/RSV-MA-Bmal2(bHLH-PAS) (Construction of Chimera Protein-Expressing Plasmid Required for Two-Hybrid Assay (Part 1))

(2-5-1) pRC/RSV-MC-mNXF (bHLH-PAS)

A plasmid pRC/RSV-MC-mNXF(bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a Gal4-mNXF) resulting from the binding between the DNA-binding region of GAL4 as a transcription regulatory factor and the bHLH-PAS region part of a present transcription regulatory factor (mNXF) was produced as described below. A pGEM-mNXF prepared in EXAMPLE 1 was cleaved with SacI and ApaI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.8 kbp: containing the bHLH-PAS region part of the present transcription regulatory factor(mNXF)). The DNA fragment thus purified and recovered was used as an insert fragment. A pRC/RSV-MC which had been cleaved with pmaCI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-MC-mNXF(bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the mNXF-encoding DNA translation part with the frame of the Gal4-DBD-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-5-2) pRC/RSV-MC-Arnt1(bHLH-PAS)

A plasmid pRC/RSV-MC-Arnt1(bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a Gal4-Arnt1) resulting from the binding between the DNA-binding region of GAL4 as a transcription regulatory factor and the bHLH-PAS region part of a present ARNT transcription coupling factor Arnt1 was produced as described below.

A pBlue-hArnt1kozac prepared in the section (2-4-1) described above was cleaved with NotI and NaeI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.8 kbp: containing the bHLH-PAS region part of Arnt1). The DNA fragment thus purified and recovered was used as an insert fragment. A pRC/RSV-MC which had been cleaved with pmaCI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-MC-Arnt1(bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Arnt1-encoding DNA translation part with the frame of the Gal4-DBD-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-5-3) pRC/RSV-MC-Arnt2(bHLH-PAS)

A plasmid pRC/RSV-MC-Arnt2(bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a Gal4-Arnt2) resulting from the binding between the DNA-binding region of GAL4 as a transcription regulatory factor and the bHLH-PAS region part of a present ARNT transcription coupling factor Arnt2 was produced as described below.

A pBlue-hArnt2kozac prepared in the section (2-4-2) described above was cleaved with NotI and BglII and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.5 kbp: containing the bHLH-PAS region part of Arnt2). The DNA fragment thus purified and recovered was used as an insert fragment. A pRC/RSV-MC which had been cleaved with pmaCI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-MC-Arnt2(bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Arnt2-encoding DNA translation part with the frame of the Gal4-DBD-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-5-4) pRC/RSV-MB-Arnt3(bHLH-PAS)

A plasmid pRC/RSV-MC-Arnt3(bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a Gal4-Arnt3) resulting from the binding between the DNA-binding region of GAL4 as a transcription regulatory factor and the bHLH-PAS region part of a present ARNT transcription coupling factor Arnt3 was produced as described below.

A pBlue-hArnt3kozac prepared in the section (2-4-3) described above was cleaved with NotI and SphI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.3 kbp: containing the bHLH-PAS region part of Arnt3). The DNA fragment thus purified and recovered was used as an insert fragment. A pRC/RSV-MB which had been cleaved with pmaCI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-MB-Arnt3(bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Arnt3-encoding DNA translation part with the frame of the Gal4-DBD-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-5-5) pRC/RSV-MA-Bmal2(bHLH-PAS)

A plasmid pRC/RSV-MA-Bmal2(bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a Gal4-Bmal2) resulting from the binding between the DNA-binding region of GAL4 as a transcription regulatory factor and the bHLH-PAS region part of a transcription coupling factor Bmal2 was produced as described below.

A pGEM-hBmal2kozac prepared in the section (2-4-4) described above was cleaved with NotI and AccI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.25 kbp: containing the bHLH-PAS region part of Bmal2). The DNA fragment thus purified and recovered was used as an insert fragment. A pRC/RSV-MA which had been cleaved with pmaCI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-MA-Bmal2 (bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Bmal2-encoding DNA translation part with the frame of the Gal4-DBD-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6) Preparation of pVP16-Arnt1 (bHLH-PAS), pVP16-Arnt2 (bHLH-PAS), pVP16-Arnt3 (bHLH-PAS), pVP16-BMAL2(bHLH-PAS), pVP16-Sim2 (bHLH-PAS), pVP16-Clock (bHLH-PAS), pVP16-NXF (bHLH-PAS) and pVP16-CP (Construction of Chimera Protein-Expressing Plasmid Required for Two-Hybrid Assay (Part 2)) (2-6-1) pVP16-Arnt1 (bHLH-PAS)

A plasmid pVP16-Arnt1 (bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a VP16-Arnt1) resulting from the binding between the Vp16 transcription activating region and the bHLH-PAS region part of a transcription coupling factor Arnt1 was produced as described below.

A pBlue-hArnt1kozac prepared in the section (2-4-1) described above was cleaved with NotI and NaeI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.8 kbp: containing the bHLH-PAS region part of Arnt1). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with BamHI and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-Arnt1 (bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Arnt1-encoding DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-2) pVP16-Arnt2 (bHLH-PAS)

A plasmid pVP16-Arnt2 (bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a VP16-Arnt2) resulting from the binding between the Vp16 transcription activating region and the bHLH-PAS region part of a present ARNT transcription coupling factor Arnt2 was produced as described below.

A pBlue-hArnt2kozac prepared in the section (2-4-2) described above was cleaved with NotI and BglII and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.5 kbp: containing the bHLH-PAS region part of Arnt2). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with BamHI and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-Arnt2 (bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Arnt2-encoding DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-3) pVP16-Arnt3 (bHLH-PAS)

A plasmid pVP16-Arnt3 which expresses a chimera protein (hereinafter sometimes designated as a VP16-Arnt3) resulting from the binding between the Vp16 transcription activating region and the full length present ARNT transcription coupling factor Arnt3 containing the bHLH-PAS region part was produced as described below.

A pBlue-hArnt3kozac prepared in the section (2-4-3) described above was cleaved with NotI and XbaI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.8 kbp: containing the full length Arnt3). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with EcoRI and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-Arnt3. The correct construction of this plasmid and the agreement of the frame of the Arnt3-encoding DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-4) pVP16-BMAL2 (bHLH-PAS)

A plasmid pVP16-Bmal2 which expresses a chimera protein (hereinafter sometimes designated as a VP16-Bmal2) resulting from the binding between the Vp16 transcription activating region and the full length transcription coupling factor Bmal2 containing the bHLH-PAS region part was produced as described below.

A pGEM-hBmal2kozac prepared in the section (2-4-4) described above was cleaved with NotI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.7 kbp: containing the full length Bmal2). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with HindIII and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-Bmal2. The correct construction of this plasmid and the agreement of the frame of the Bmal2-encoding DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-5) pVP16-Sim2 (bHLH-PAS)

A plasmid pVP16-Sim2 (bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a VP16-Sim2) resulting from the binding between the Vp16 transcription activating region and the bHLH-PAS region part of Sim2 was produced as described below. A pRC/RSV-hSim2kozac prepared in the section (2-4-5) described above was cleaved with NotI and BamHI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.5 kbp: containing the bHLH-PAS region part of Sim2). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with BamHI and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-Sim2 (bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Sim2-encoding DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-6) pVP16-Clock (bHLH-PAS)

A plasmid pVP16-Clock (bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a VP16-Clock) resulting from the binding between the Vp16 transcription activating region and the bHLH-PAS region part of Clock was produced as described below.

A pBlue-hClock kozac prepared in the section (2-4-6) described above was cleaved with HicII and NcoI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.6 kbp: containing the bHLH-PAS region part of Clock). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with BamHI and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-Clock (bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the Clock-encoding DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-7) pVP16-NXF (bHLH-PAS)

A plasmid pVP16-NXF (bHLH-PAS) which expresses a chimera protein (hereinafter sometimes designated as a VP16-NXF) resulting from the binding between the Vp16 transcription activating region and the bHLH-PAS region part of a present transcription activating factor (mNXF) was produced as described below.

A pGEM-mNXF prepared in EXAMPLE 1 was cleaved with SacI and ApaI and imparted with a blunt end using a T4 polymerase, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to purify and recover a DNA fragment (about 1.8 kbp: containing the bHLH-PAS region part of a present transcription activating factor (mNXF)). The DNA fragment thus purified and recovered was used as an insert fragment. A pVP16 vector (purchased from Clontech) which had been cleaved with BamHI and then subjected to a BAP treatment and then further imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVP16-NXF (bHLH-PAS). The correct construction of this plasmid and the agreement of the frame of the present transcription activating factor (mNXF) DNA translation part with the frame of the VP16 transcription activating region-encoding DNA were verified by investigating the nucleotide sequence of the binding part and the nucleotide sequence of the translation part.

(2-6-8) pVP16-CP

A plasmid pVP16-CP which expresses a chimera protein of a virus core protein with V16 was purchased from Clontech. Since this protein has no relationship with the bHLH-PAS family, it does not bind to a transcription regulatory factor of the bHLH-PAS family. Accordingly, this plasmid was employed as a negative control plasmid in the test described in the section (2-6) shown below.

(2-7) Two-Hybrid Assay for Verifying Formation of Complex of Present ARNT Transcription Coupling Factor with Present Transcription Regulatory Factor

About 5×10⁶ HeLa cells were cultured in a 10% FBS-supplemented DMEM medium (NISSUI SEIYAKU) at 37° C. in the presence of 5% CO₂ in a petri dish (Falcon) whose diameter was about 10 cm. On the next day, the cultured cells were dispersed by a trypsin treatment, washed twice with a FBS-free DMEM medium, and then dispersed again in a FBS-free DMEM medium at the cell density of 5×10⁶. 0.4 ml of this cell dispersion was combined with the three plasmid, namely, the reporter gene plasmid prepared in the Section (2-1) described above (pGL-TATA-Galx4) (for example 3 μg), the plasmid prepared in the Section (2-5) described above which expresses a chimera protein (for example 3 μg) and the plasmid prepared in the Section (2-6) described above which expresses a chimera protein (for example 3 μg), and the mixture was transferred into an electroporation cuvette, where a transfection was conducted by an electroporation method employing a Gene pulser (BIORAD) under the conditions involving 220V and 950 μF. After the transfection, the culture medium was replaced with a 10% FBS-supplemented DMEM, and then further cultured in a 6-well plate for about 24 hours. Then, the culture medium was removed from the wells, and the cells depositing on the plate wall were washed twice with PBS(−), and then 200 μl per well of a 5-fold diluted PGC 50 (TOYO INK) was added and allowed to stand at room temperature for 30 minutes. 20 μl Aliquots of this cell suspension were dispensed into a opaque plate (Corning International K.K), and this plate was mounted on a luminometer LB96P (Berthold Japan, Co. Ltd.) fitted with an enzyme substrate automatic injector, and after dispensing 50 μl of the substrate solution PGL100 (TOYO INK) automatically the luciferase activity of each well was determined.

As a result, it was revealed as evident from FIG. 1 that in the system employing Gal4-NXF each of VP16-Arnt1, VP16-Arnt2 and VP16-Arnt3 exhibited a binding activity (interaction) with the bHLH-PAS region part of the present transcription regulatory factor (NXF). On the other hand, none of Bmal2, Sim2 and Clock exhibited a binding activity (interaction) with the bHLH-PAS region part of the present transcription regulatory factor (NXF).

It was also revealed that no homodimer was formed between the present transcription regulatory factors (NXFs).

In addition, it was revealed as evident from FIGS. 2, 3 and 4 that in the system employing Gal4-Arnt1 (FIG. 2), Gal4-Arnt2 (FIG. 3) and Gal4-Arnt3 (FIG. 4) the inventive transcription regulatory factor (NXF) exhibited a binding activity (interaction) with the bHLH-PAS region part of any of Arnt1, Arnt2 and Arnt3.

It was also revealed here again that in the system employing Gal4-Bmal2 (FIG. 5) the present transcription regulatory factor (NXF) exhibited no binding activity (interaction) with Bmal2.

(2-8) Gel Shift Assay for Verifying DNA Binding Ability Possessed by Inventive Transcription Activating Complex

(2-8-1) Preparation of pVL1392-hArnt2kozac (Construction of Transfer Vector for Preparing Recombinant Virus Expressing Full Length Present ARNT Transcription Coupling Factor)

A transfer vector pVL1392-hArnt2kozac for producing a recombinant virus (Baculovirus) expressing a full length Arnt2 was prepared as described below.

First, the pBlue-hArnt2kozac prepared in the section (1-4) described above was cleaved simultaneously with NotI and XbaI, and then subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to recover a DNA fragment (about 2.2 kbp: containing the full length Arnt 2 translation region). The recovered DNA fragment was employed as an insert fragment.

Subsequently, a pVL1392 vector (purchased from Pharmingen) which had been cleaved with NotI and XbaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVL1392-hArnt2kozac which was a transfer vector for preparing a recombinant virus expressing the full length Arnt2. The correct construction of the translation region of the DNA encoding Arnt 2 downstream of a polyhedrin promoter was verified by investigating the nucleotide sequence of the binding part.

(2-8-2) Preparation of pVL1392-NXF (Construction of Transfer Vector for Preparing Recombinant Virus Expressing Full Length Present Transcription Regulatory Factor)

Then, a transfer vector pVL1392-rNXF for producing a recombinant virus (Baculovirus) expressing a full length present transcription regulatory factor (rNXF) was prepared as described below.

First, the pGEM-rNXF was cleaved simultaneously with ScaI and SacI and also with NotI, and then imparted with a blunt end using a T4 polymerase. The blunt-ended DNA fragment was subjected to a low melting point agarose electrophoresis (Agarose L; Nippon Gene) to recover a DNA fragment (about 2.5 kbp: containing the full length Arnt translation region of the present transcription regulatory factor (NXF)). The recovered DNA fragment was employed as an insert fragment.

Subsequently, a pVL1393 vector (purchased from Pharmingen) which had been cleaved with SmaI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pVL1392-rNXF which was a transfer vector for preparing a recombinant virus expressing the present transcription regulatory factor (rNXF).

The correct construction of the translation region of the translation region of the present transcription regulatory factor (rNXF) downstream of a polyhedrin promoter was verified by investigating the nucleotide sequence of the binding part.

The pGEN-rNXF employed as described above was prepared by the method similar to that employed for preparing pGEM-mNXF described in EXAMPLE 1 except for using as a template a rat Brain cDNA library instead of the mouse Brain cDNA library.

(2-8-3) Preparation of Recombinant Virus Particle Comprising Present ARNT Transcription Coupling Factor Arnt2 or Present Transcription Regulatory Factor (rNXF) Introduced Therein

An insect cell line Sf21 (purchased from Invitrogen) was cultured in a 10% FCS (fetal calf serum), 0.33% yeast hydrolysate, 0.33% lactoalbumin hydrolysate-supplemented Grace medium (purchased from Gibco) in an ordinary atmospheric environment at 27° C. The cultured cell was introduced with a transfer vector for preparing a recombinant virus and a Baculovirus genome DNA as described below.

First, 10⁶ cells were inoculated into the wells of a 6-well plate and allowed to stand for 2 hours. After ensuring the adhesion of the cells, the culture medium in each well was replaced with 0.8 ml of a serum-free Grace medium. To the cells thus prepared, a mixture prepared by mixing 0.25 μg of linear Baculovirus genome DNA (Baculo Gold DNA; purchased from Pharmingen) and 2 μg of the transfer vector for preparing the recombinant virus with 200 μl of the serum-free medium, adding 6 μl of a Cell Fectin reagent (purchased from Gibco) and allowing to stand at room temperature for 15 minute was added. After 5 hours, the culture medium in each well was replaced with an ordinary serum-containing Grace medium and incubated continuously for 72 hours. As a result of a homologous recombination of the transfer vector for preparing the recombinant virus and the Baculovirus genome DNA, a recombinant virus particle in which the present ARNT transcription coupling factor Arnt2-encoding DNA or the present transcription regulatory factor (rNXF) was integrated into the downstream of a promoter possessed by a polyhedrin protein gene derived from the Baculovirus was obtained. As a control, a commercially available wild baculovirus (non-recombinant virus, purchased from Pharmingen) was employed.

(2-8-4) Preparation of Whole Cell Extract Containing Present ARNT Transcription Coupling Factor Arnt2 or Present Transcription Regulatory Factor (NXF)

A whole cell extract containing a present ARNT transcription coupling factor Arnt2 or a present transcription regulatory factor (NXF) was prepared as described below.

First, 10⁶ cells of insect cell line SF21 in a T50 flask were infected with the recombinant virus particle prepared in the section (2-8-3) described above. 72 hours after the infection, the cells were centrifuged at 1000 G for 2 minutes to recover the cell pellets. The recovered cell pellets were homogenized by a pipetting operation in a buffer whose volume was 4 times that of the cells and which contained 20 mM HEPS (pH7.9), 300 mM NaCl and 20% Glycerol, and allowed to stand on ice for 30 minutes. Subsequently, it was centrifuged at 10000 G for 1 hour to recover the supernatant. This supernatant was employed in the following tests as a whole cell extract containing a present RNT transcription coupling factor Arnt2 or a present transcription regulatory factor (NXF).

(2-8-5) Gel Shift Assay

A gel shift assay was conducted as described below.

First, a CME double-stranded oligonucleotide was prepared by hybridizing two oligonucleotides (SEQ ID No.49: 5′-ctagaaatttgtacgtgccacaga-3′, SEQ ID No.50:5′-tctgtggcacgtacaaatttctag-3′). On the other hand, an E-Box double-stranded oligonucleotide (a DNA which has a nucleotide sequence containing a single nucleotide substitution in a CME core sequence and to which Sim2 and Arnt2 are no longer bound) was prepared by hybridizing two oligonucleotides (SEQ ID No.51: 5′-caagtccacgtgcaggga-3′, SEQ ID No.52: 5′-tccctgcacgtggacttg-3′).

2 μg of the CME double-stranded oligonucleotide thus prepared was reacted in the presence of 10U of a T4 kinase and 3.7 MBq of [γ-³²P]-ATP (AA0018; Amarsham Pharmacia) at 37° C. for 1 hour to radiolabel its 5′ terminal. This was centrifuged at 1000 G for 2 minutes using a spin column (ProbeQuant G50 micro columns; Amersham Pharmacia) to obtain as a passing-through fraction a radiolabeled CME double-stranded oligonucleotide which was free from any excessive radioactive substrate. The radiolabeled CME double-stranded oligonucleotide thus obtained was employed at about 10⁴ DPM/group as a hot probe DNA in the gel shift assay described below. The binding with the hot probe DNA in the gel shift assay was conducted by incubating a reaction solution containing 20 mM HEPES (pH7.9), 100 mM NaCl, 1 mM DTT, 5% Glycerol, 0.1 μg/μl Poly [dI-dC] and 1 μg of the whole cell extract prepared in the section (2-8-4) described above at 25° C. for 30 minutes. When a Cold probe DNA was added as a competitor to the binding reaction system, it was allowed to coexist in the binding reaction system in an amount which was 100 times the amount of the hot probe DNA. The binding reaction product formed as a result of the binding reaction described above was subjected to a 5% (acrylamide:bis=39:1) polyacrylamide gel electrophoresis using 0.5×TBE buffer. After the electrophoresis, the gel was brought into a close contact with a 3MMChr filter paper, which was dried and then used to expose an IP plate (FUJI, FILM) for about 3 hours. The radio-exposed IP plate was subjected to an imaging analyzer (FUJI FILM) to read the radio-exposed part, whereby obtaining an gal image.

As a result, FIG. 6 clearly indicated that the band showing the binding with the hot probe DNA (i.e., radiolabeled CME double-stranded oligonucleotide) was observed only when the present transcription regulatory factor (NXF) and the Arnt transcription coupling factor Arnt2 were coexisting. On the other hand, the band disappeared when allowing a large excess of the non-radiolabeled CME double-stranded oligonucleotide as a cold probe DNA to coexist in the binding reaction system, but did not disappeared even when allowing a large excess of the non-radiolabeled E-box double-stranded oligonucleotide as a cold probe DNA to coexist in the binding reaction system, revealing that the band was not bound to the E-box sequence but was bound specifically only to the CME sequence.

As described above, the inventive transcription activating complex was proven to be bound specifically only to the CME sequence (i.e., a DNA region to which the transcription inhibiting complex of the Arnt transcription coupling factor with the transcription regulatory factor Sim2 can be bound).

(2-9) Luciferase Assay Using CME Sequence Responsive Reporter for Verifying Transcription Promoting Ability Possessed by Inventive Transcription Activating Complex

(2-9-1) Preparation of pRC/RSV-hArnt2kozac

A plasmid for expressing a full length Arnt2 in a mammalian cell was prepared as described below.

First a pBlue-hArnt2kozac was cleaved simultaneously with NotI and XbaI, subjected to a low melting point agarose electrophoresis (agarose L; Nippon Gene) to recover a DNA fragment (about 2.2 kbp) containing a full length translation region of a DNA encoding Arnt2. The recovered DNA fragment was employed as an insert fragment.

Then, a pRC/RVS (purchased from Invitrogen) which had been cleaved with NotI and XbaI and then subjected to a BAP treatment was employed as a vector. This vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to prepare a pRC/RSV-hArnt2kozac which was a plasmid for expressing the full length Arnt2 in a mammalian cell (i.e., full length Arnt 2 mammalian cell expression plasmid).

(2-9-2) Preparation of pRC/RSV-mNXFsense (and pRC/RSV-mNXFantisense)

Then, a plasmid for expressing a full length present transcription regulatory factor (mNXF) in a mammalian cell was prepared as described below.

First, the direction of the insertion fragment in relation with the multiple cloning site of the pGEM-mNXF was in such a construction that the Sp6 promoter of a commercial pGEM vector was positioned upstream of the initiation codon. Then 1 μg of this pGEM-mNXF was employed as a template together with two oligonucleotide primers (forward primer 5′-gggcgctgcagcccagccaccatgtaccgatccaccaaggg-3′ (SEQ ID No.53), reverse primer 5′-aatctcggcgttgatctggt-3′ (SEQ ID No.54) to effect a PCR using a KODplus polymerase (TOYOBO), whereby a partial fragment of the present transcription regulatory factor (mNXF) DNA into which a Kozac sequence (5′-CCAGCCACC-3′) immediately before the initiation codon of the present transcription regulatory factor (mNXF) and a PstI restriction enzyme site upstream thereof had been introduced. The PCR conditions employed 35 cycles, each cycle involving an incubation at 95° C. for 1 minutes followed by 55° C. for 30 seconds followed by 72° C. for 1 minutes. The amplified DNA fragment thus obtained was cleaved with PstI and BssHII, and subjected to a low melting point agarose gel electrophoresis (NusieveGTG agarose; FMCbio), whereby accomplishing the purification and recovery. The DNA fragment thus purified and recovered was used as an insert fragment. Then, a GEM-mNXF which had been cleaved with PstI and BssHII and then BAP-treated was subjected to a low melting point agarose gel electrophoresis (Agarose L, Nippon Gene) to recover a DNA fragment. The recovered DNA fragment (0.1 μg) was used as a vector. This vector was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to obtain a pGEM-mNXF kozac into which a Kozac sequence (5′-CCAGCCACC-3′) had been introduced immediately before the initiation codon of the present transcription regulatory factor (mNXF). The nucleotide sequence of the insert fragment was verified to be correct using a DNA sequencer (Model 3700; PE biosystems).

Then, this pGEM-mNXF kozac was cleaved simultaneously with 3 enzymes PstI, NotI and ScaI, and then subjected to a low melting point agarose electrophoresis to recover an mNXF kozac PstI-NotI-cleaved DNA fragment (about 2.5 kbp). The recovered DNA fragment was imparted with a blunt end using a T4 polymerase and then used as an insert fragment. After cleaving an RSV promoter-carrying pRC/RSV (Invitrogen) was cleaved with HindIII, imparted with a blunt end using a T4 polymerase, and subjected to a BAP treatment, whereby obtaining a vector. This vector (0.1 μg) was ligated with the insert fragment (0.5 μg) described above using a T4 Ligase to obtain (a) a pRC/RSV-mNXFsense which is a plasmid expressing the sense strand of the mNXF kozac under the control of the RSV promoter and (b) a pRC/RVS-mNXFantisense which is a plasmid expressing the antisense strand of the mNXF kozac under the control of the RSV promoter. Whether the prepared plasmid was the desired plasmid or not was checked by investigating the nucleotide sequence of the margin between the vector and the inserted fragment. Among these plasmids, only the pRC/RSV-mNXFsense was employed in the following tests as a plasmid for expressing the present transcription regulatory factor (mNXF) in a mammalian cell.

(2-9-3) Preparation of pRC/RSV-hSim2kozac

As a plasmid expressing Sim2 in a mammalian cell, a pRC/RSV-hSim2kozac prepared in the section (2-4-5) described above was employed.

(2-9-4) Preparation of pRC/RSV-hClock kozac

A plasmid expressing Clock was prepared as described below.

First, a pBlue-hClock kozac was cleaved by the both restriction enzymes, i.e., EcoRV and SpeI. This was imparted with a blunt end using a T4 polymerase, and subjected to a low melting point agarose electrophoresis to recover a DNA fragment (about 2.5 kbp: containing clock translation sequence). The recovered DNA fragment was employed as an insert fragment. A pRC/RSV vector which had been cleaved with HindIII and then imparted with a blunt end using a T4 polymerase was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) using a T4 Ligase, whereby obtaining a pRC/RSV-hClock kozac.

(2-9-5) Preparation of pGL3-TATA-CMEx4

A reporter gene plasmid comprising 4 copies of a CME sequence (i.e., a DNA region to which Sim1 or Sim2 can be bound) upstream of a luciferase gene comprising a TATA minimum promoter was prepared as described below.

First, a double-stranded oligonucleotide was prepared by hybridizing two oligonucleotides (SEQ ID No.55: 5′-ctagcctagaaatttgtacgtgccacagactagaaatttgtacgtgccacagag-3′, SEQ ID No.56: 5′-ctagctctgtggcacgtacaaatttctagtctgtggcacgtacaaatttctagg-3′). The resultant double-stranded oligonucleotide had 2 copies of a CME sequence (i.e., a DNA region to which Sim1 or Sim2 can be bound) and has a sticky end capable of binding to a NheI restriction enzyme cleavage fragment. The terminal of this oligonucleotide was phosphorylated using a T4 kinase, and connected in tandem using a T4 Ligase to obtain a binding reaction product. The resultant binding reaction product was subjected to a low melting point agarose gel electrophoresis (NusieveGTG agarose; FMCbio) to recover a DNA fragment in which two double-stranded oligonucleotides were connected in tandem. The recovered DNA fragment was used as an insert fragment. A pGL3-TATA vector which had been cleaved with NheI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) using a T4 Ligase to prepare a pGL3-TATA-CMEx4 which is a reporter gene plasmid comprising 4 copies of the CME sequence (i.e., a DNA region to which Sim1 or Sim2 can be bound) upstream of a luciferase gene comprising a TATA minimum promoter. The correct construction was verified by investigating the nucleotide sequence of the promoter part.

(2-9-6) Preparation of pGL3-TATA-(Ebox)x3

A reporter gene plasmid comprising an E-box upstream of a luciferase gene comprising a TATA minimum promoter was prepared as described below.

First, a double-stranded oligonucleotide was prepared by hybridizing two oligonucleotides (SEQ ID No.57: 5′-ctttagccacgtgacagtgtaagcacacgtgggccctcaagtccacgtgcagggac-3′: SEQ ID No.58: 5′-tcgagtccctgcacgtggacttgagggcccacgtgtgcttacactgtcacgtggctaaaggtac-3′). The resultant double-stranded oligonucleotide had 3 copies of a Clock responsive sequence (i.e., E-box: Science (1998) 280, 1564-1567, N. Gekakis et. al.) and has a sticky end capable of binding to a KpnI and XhoI restriction enzyme cleavage fragment. The terminal of this oligonucleotide was phosphorylated using a T4 kinase, used as an insert fragment. A pGL3-TATA vector which had been cleaved with KpnI and XhoI and then subjected to a BAP treatment was employed as a vector, and this vector (0.1 μg) was ligated with the insert fragment (0.5 μg) using a T4 Ligase to prepare a pGL3-TATA-(Ebox)x3 which is a reporter gene plasmid comprising 3 copies of the Clock responsive sequence (i.e., E-box) upstream of a luciferase gene comprising a TATA minimum promoter. The correct construction was verified by investigating the nucleotide sequence of the promoter part.

(2-9-7) Reporter Assay for Verifying Transcription Promoting Ability of Inventive Transcription Activating Complex

About 5×10⁶ HeLa cells were cultured in a 10% FBS-supplemented DMEM medium (NISSUI SEIYAKU) at 37° C. in the presence of 5% CO₂ in a petri dish (Falcon) whose diameter was about 10 cm. On the next day, the cultured cells were dispersed by a trypsin treatment, washed twice with a FBS-free DMEM medium, and then dispersed again in a FBS-free DMEM medium at the cell density of 5×10⁶. 0.4 ml of this cell dispersion was mixed with an appropriate combination (detailed in the table shown below) of the three plasmid, namely, the reporter gene plasmid prepared in the Section (2-9-5, 6) described above (for example 3 μg), the plasmid prepared in the Section (2-9-1, 2) described above which expresses a protein (for example 3 μg) and the plasmid prepared in the Section (2-9-3, 4) described above which expresses a protein (for example 3 μg), and the mixture was transferred into an electroporation cuvette, where a transfection was conducted by an electroporation method employing a Gene pulser (BIORAD) under the conditions involving 220V and 950 μF. After the transfection, the culture medium was replaced with a 10% FBS-supplemented DMEM, and then further cultured in a 6-well plate for about 24 hours.

TABLE 1 Plasmid combination: Amount (μg) Total amount FIG. Abscissa Reporter (pRC/RSV as No. Column Clock Sim2 mNXF Arnt2 gene remainder) FIG. A 0 0 0 2 2 9 7 B 0 0 1 2 2 9 C 0 0 2 2 2 9 D 0 0 3 2 2 9 E 0 0 2 2 2 9 F 0 1 2 2 2 9 G 0 2 2 2 2 9 H 0 3 2 2 2 9 I 0 0 2 2 2 9 J 1 0 2 2 2 9 K 2 0 2 2 2 9 L 3 0 2 2 2 9 Total amount Reporter (pRC/RSV as Column Sim2 mNXF Arnt2 gene remainder) FIG. a 0 2 2 2 9 8 b 2 0 2 2 9 c 2 1 2 2 9 d 2 2 2 2 9 e 2 3 2 2 9

Then, the culture medium was removed from the wells, and the cells depositing on the plate wall were washed twice with PBS(−), and then 200 μl per well of a 5-fold diluted PGC 50 (TOYO INK) was added and allowed to stand at room temperature for 30 minutes. 20 μl Aliquots of this cell suspension were dispensed into a opaque plate (Corning International K.K), and this plate was mounted on a luminometer LB96P (Berthold Japan, Co. Ltd.) fitted with an enzyme substrate automatic injector, and after dispensing 50 μl of the substrate solution PGL100 (TOYO INK) automatically the luciferase activity of each well was determined.

As evident from FIG. 7, the expression of the reporter gene controlled by the E-box sequence as a Clock responsive sequence was not influenced in the case of (a) the expression only of Arnt2 which is a present ARNT transcription coupling factor, (b) the expression only of the present transcription regulatory factor (NXF) or (c) the expression of the inventive transcription activating complex (i.e., co-expression of Arnt2 which is a present ARNT transcription coupling factor and the present transcription regulatory factor (NXF)).

On the other hand, the expression of the reporter gene controlled by the CEM sequence was not influenced in the cases of (a′) the expression only of Arnt2 which is a present ARNT transcription coupling factor or (b′) the expression only of the present transcription regulatory factor (NXF), but reflected a potent transcription promoting ability in the case of (c′) the expression of the inventive transcription activating complex (i.e., co-expression of Arnt2 which is a present ARNT transcription coupling factor and the present transcription regulatory factor (NXF)).

Accordingly, it was revealed that the DNA region to which the inventive transcription activating complex can be bound is identical to the CME sequence, and the inventive transcription activating complex has a transcription promoting effect on the promoter containing the CME sequence.

FIG. 8 also indicates that the present transcription regulatory factor (NXF) activated the transcription of the reporter gene in a dose-dependent manner in the presence of Arnt2 which is a present ARNT transcription coupling factor (see, A, B, C, D in FIG. 8). In the system where the transcription activity once increased by the present transcription activating complex was then exposed to the added Sim2 (E, F, G, H in FIG. 8), a dose dependent inhibition of the reporter gene transcription was noted. In the system where a negative control Clock was added instead of Sim2 (I, J, K, L in FIG. 8), no inhibition on the reporter gene transcription was noted,

Furthermore, FIG. 9 revealed that in the system where the transcription activity once inhibited by the addition of Sim2 in the presence of Arnt2 was then exposed to the added present transcription regulatory factor (mNXF) (b, c, d, e in FIG. 9), a release from the inhibition of the transcription by Sim2 was observed in a dose dependent manner, resulting in the change in the condition toward the transcription activation. Thus, a release from the Sim2-induced inhibition of the transcription of the reporter gene operably connected to the promoter containing the CME sequence was confirmed.

INDUSTRIAL APPLICABILITY

The present invention is successful in providing a transcription activating complex in which a transcription regulatory factor/ARNT family transcription coupling factor heterodimer complex exhibits a promotive action on the CME sequence. By allowing the transcription activating complex to act competitively with a Sim2/ARNT family transcription coupling factor heterodimer complex, a therapy in a Down's syndrome patient is expected.

Free Text in Sequence Listing

SEQ ID No.7

Designed oligonucleotide primer for PCR

SEQ ID No.8

Designed oligonucleotide primer for PCR

SEQ ID No.9

Designed oligonucleotide primer for PCR

SEQ ID No.10

Designed oligonucleotide primer for PCR

SEQ ID No.11

Designed oligonucleotide for DNA region to which the protein can be bound

SEQ ID No.12

Designed oligonucleotide for DNA region to which the protein can be bound

SEQ ID No.13

Designed oligonucleotide for DNA region to which the protein can be bound

SEQ ID No.14

Designed oligonucleotide for DNA region to which the protein can be bound

SEQ ID No.15

Designed oligonucleotide for DNA region to which the protein can be bound

SEQ ID No.16

Designed oligonucleotide for DNA region to which the protein can be bound

SEQ ID No.17

Designed oligonucleotide for plasmid construction

SEQ ID No.18

Designed oligonucleotide for plasmid construction

SEQ ID No.19

Designed oligonucleotide for plasmid construction

SEQ ID No.20

Designed oligonucleotide for plasmid construction

SEQ ID No.21

Designed oligonucleotide for plasmid construction

SEQ ID No.22

Designed oligonucleotide for plasmid construction

SEQ ID No.23

Designed oligonucleotide for plasmid construction

SEQ ID No.24

Designed oligonucleotide for plasmid construction

SEQ ID No.25

Designed oligonucleotide primer for PCR

SEQ ID No.26

Designed oligonucleotide primer for PCR

SEQ ID No.27

Designed oligonucleotide primer for PCR

SEQ ID No.28

Designed oligonucleotide primer for PCR

SEQ ID No.29

Designed oligonucleotide primer for PCR

SEQ ID No.30

Designed oligonucleotide primer for PCR

SEQ ID No.31

Designed oligonucleotide primer for PCR

SEQ ID No.32

Designed oligonucleotide primer for PCR

SEQ ID No.33

Designed oligonucleotide primer for PCR

SEQ ID No.34

Designed oligonucleotide primer for PCR

SEQ ID No.35

Designed oligonucleotide primer for PCR

SEQ ID No.36

Designed oligonucleotide primer for PCR

SEQ ID No.37

Designed oligonucleotide primer for PCR

SEQ ID No.38

Designed oligonucleotide primer for PCR

SEQ ID No.39

Designed oligonucleotide primer for PCR

SEQ ID No.40

Designed oligonucleotide primer for PCR

SEQ ID No.41

Designed oligonucleotide primer for PCR

SEQ ID No.42

Designed oligonucleotide primer for PCR

SEQ ID No.43

Designed oligonucleotide primer for PCR

SEQ ID No.44

Designed oligonucleotide primer for PCR

SEQ ID No.45

Designed oligonucleotide primer for PCR

SEQ ID No.46

Designed oligonucleotide primer for PCR

SEQ ID No.47

Designed oligonucleotide primer for PCR

SEQ ID No.48

Designed oligonucleotide primer for PCR

SEQ ID No.49

Designed oligonucleotide for a CME double-stranded oligonucleotide

SEQ ID No.50

Designed oligonucleotide for a CME double-stranded oligonucleotide

SEQ ID No.51

Designed oligonucleotide for a E-box double-stranded oligonucleotide

SEQ ID No.52

Designed oligonucleotide for a E-box double-stranded oligonucleotide

SEQ ID No.53

Designed oligonucleotide primer for PCR

SEQ ID No.54

Designed oligonucleotide primer for PCR

SEQ ID No.55

Designed oligonucleotide for plasmid construction

SEQ ID No.56

Designed oligonucleotide for plasmid construction

SEQ ID No.57

Designed oligonucleotide for plasmid construction

SEQ ID No.58

Designed oligonucleotide for plasmid construction 

1. An in vitro complex of a transcription coupling factor of any one of ARNT 1 to 3 and a transcription regulatory factor comprising any of the amino acid sequences shown below, which is a transcription activating complex that binds to a DNA region (5′-ACGTG-3′, SEQ ID NO: 16) in competition with a transcription inhibiting complex of a Sim2 as a transcription regulatory factor and a transcription coupling factor of any one of ARNT 1 to 3 and which promotes transcription of a gene located downstream of the DNA region, wherein the amino acid sequences are: (a) the amino acid sequence represented by any one of SEQ ID NOs: 1 to 3, (b) an amino acid sequence of a protein comprising an amino acid sequence exhibiting an amino acid identity of 90% or more to the amino acid sequence represented by any of SEQ ID NOs: 1 to 3 and regulates transcription of a gene located downstream of a DNA region comprising the nucleotide sequence of SEQ ID NO:16.
 2. An in vitro host cell obtained by introducing one or more vectors encoding a transcription activating complex according to claim
 1. 3. An in vitro host cell obtained by introducing a single vector comprising both of the DNAs shown below or several vectors comprising such DNAs independently into a host cell, wherein the DNAs are: (1) a DNA comprising a nucleotide sequence encoding an amino acid sequence of a transcription coupling factor of any one of ARNT 1 to 3, and (2) a DNA comprising a nucleotide sequence encoding any of the amino acid sequences shown below: (a) the amino acid sequence represented by any one of SEQ ID NOs: 1 to 3, (b) an amino acid sequence of a protein comprising an amino acid sequence exhibiting an amino acid identity of 90% or more to the amino acid sequence represented by any one of SEQ ID NOs: 1 to 3 and also having an ability to regulate transcription of a gene located downstream of a DNA region comprising the nucleotide sequence of SEQ ID NO:16.
 4. An in vitro host cell according to claim 2 or 3 further containing a DNA of a reporter gene comprising a promoter, as being operably connected thereto, said promoter contains DNA region (5′-ACGTG-3, SEQ ID NO: 16) to which the transcription inhibiting complex of a Sim2 as a transcription regulatory factor and a transcription coupling factor of any one of ARNT 1 to 3 can be bound.
 5. A method to evaluate regulation of transcription, an in vitro complex of a transcription coupling factor of any one of ARNT 1 to 3 and a transcription regulatory factor comprising any of the amino acid sequences shown below, which is a transcription activating complex that binds to a DNA region (5′-ACGTG-3′, SEQ ID NO: 16) in competition with a transcription inhibiting complex of a Sim2 as a transcription regulatory factor and a transcription coupling factor of any one of ARNT 1 to 3 and which promotes transcription of a gene located downstream of the DNA region, wherein the amino acid sequences are: (a) the amino acid sequence represented by any one of SEQ ID NOs: 1 to 3, (b) an amino acid sequence of a protein comprising an amino acid sequence exhibiting an amino acid identity of 90% or more to the amino acid sequence represented by any of SEQ ID NOs: 1 to 3 and regulates transcription of a gene located downstream of a DNA region comprising the nucleotide sequence of SEQ ID NO: 16 which comprises: (1) contacting a test substance with an in vitro host cell according to claim 4; (2) measuring an expression level of the reporter gene possessed by the in vitro host cell; and, (3) evaluating the substance for its ability of regulating the transcription promoting ability possessed by the transcription activating complex based on the expression level correlating with the level measured in (2).
 6. A searching method comprising selecting a substance having an ability to regulate the transcription promoting ability possessed by the transcription activating complex based on a regulating ability evaluated by the method according to claim
 5. 